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Rezaeeyan H, Arabfard M, Rasouli HR, Shahriary A, Gh BFNM. Evaluation of common protein biomarkers involved in the pathogenesis of respiratory diseases with proteomic methods: A systematic review. Immun Inflamm Dis 2023; 11:e1090. [PMID: 38018577 PMCID: PMC10659759 DOI: 10.1002/iid3.1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/22/2023] [Accepted: 11/04/2023] [Indexed: 11/30/2023] Open
Abstract
AIM Respiratory disease (RD) is one of the most common diseases characterized by lung dysfunction. Many diagnostic mechanisms have been used to identify the pathogenic agents of responsible for RD. Among these, proteomics emerges as a valuable diagnostic method for pinpointing the specific proteins involved in RD pathogenesis. Therefore, in this study, for the first time, we examined the protein markers involved in the pathogenesis of chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), asthma, bronchiolitis obliterans (BO), and chemical warfare victims exposed to mustard gas, using the proteomics method as a systematic study. MATERIALS AND METHODS A systematic search was performed up to September 2023 on several databases, including PubMed, Scopus, ISI Web of Science, and Cochrane. In total, selected 4246 articles were for evaluation according to the criteria. Finally, 119 studies were selected for this systematic review. RESULTS A total of 13,806 proteins were identified, 6471 in COPD, 1603 in Asthma, 5638 in IPF, three in BO, and 91 in mustard gas exposed victims. Alterations in the expression of these proteins were observed in the respective diseases. After evaluation, the results showed that 31 proteins were found to be shared among all five diseases. CONCLUSION Although these 31 proteins regulate different factors and molecular pathways in all five diseases, they ultimately lead to the regulation of inflammatory pathways. In other words, the expression of some proteins in COPD and mustard-exposed patients increases inflammatory reactions, while in IPF, they cause lung fibrosis. Asthma, causes allergic reactions due to T-cell differentiation toward Th2.
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Affiliation(s)
- Hadi Rezaeeyan
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion MedicineIranian Blood Transfusion Organization (IBTO)TehranIran
| | - Masoud Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Hamid R. Rasouli
- Trauma Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Alireza Shahriary
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - B. Fatemeh Nobakht M. Gh
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
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2
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Vizuet-de-Rueda JC, Montero-Vargas JM, Galván-Morales MÁ, Porras-Gutiérrez-de-Velasco R, Teran LM. Current Insights on the Impact of Proteomics in Respiratory Allergies. Int J Mol Sci 2022; 23:ijms23105703. [PMID: 35628512 PMCID: PMC9144092 DOI: 10.3390/ijms23105703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Respiratory allergies affect humans worldwide, causing extensive morbidity and mortality. They include allergic rhinitis (AR), asthma, pollen food allergy syndrome (PFAS), aspirin-exacerbated respiratory disease (AERD), and nasal polyps (NPs). The study of respiratory allergic diseases requires new technologies for early and accurate diagnosis and treatment. Omics technologies provide the tools required to investigate DNA, RNA, proteins, and other molecular determinants. These technologies include genomics, transcriptomics, proteomics, and metabolomics. However, proteomics is one of the main approaches to studying allergic disorders' pathophysiology. Proteins are used to indicate normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. In this field, the principal goal of proteomics has been to discover new proteins and use them in precision medicine. Multiple technologies have been applied to proteomics, but that most used for identifying, quantifying, and profiling proteins is mass spectrometry (MS). Over the last few years, proteomics has enabled the establishment of several proteins for diagnosing and treating respiratory allergic diseases.
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3
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Sim S, Choi Y, Park HS. Potential Metabolic Biomarkers in Adult Asthmatics. Metabolites 2021; 11:metabo11070430. [PMID: 34209139 PMCID: PMC8306564 DOI: 10.3390/metabo11070430] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 12/05/2022] Open
Abstract
Asthma is the most common chronic airway inflammation, with multiple phenotypes caused by complicated interactions of genetic, epigenetic, and environmental factors. To date, various determinants have been suggested for asthma pathogenesis by a new technology termed omics, including genomics, transcriptomics, proteomics, and metabolomics. In particular, the systematic analysis of all metabolites in a biological system, such as carbohydrates, amino acids, and lipids, has helped identify a novel pathway related to complex diseases. These metabolites are involved in the regulation of hypermethylation, response to hypoxia, and immune reactions in the pathogenesis of asthma. Among them, lipid metabolism has been suggested to be related to lung dysfunction in mild-to-moderate asthma. Sphingolipid metabolites are an important mediator contributing to airway inflammation in obese asthma and aspirin-exacerbated respiratory disease. Although how these molecular variants impact the disease has not been completely determined, identification of new causative factors may possibly lead to more-personalized and precise pathway-specific approaches for better diagnosis and treatment of asthma. In this review, perspectives of metabolites related to asthma and clinical implications have been highlighted according to various phenotypes.
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Affiliation(s)
| | | | - Hae-Sim Park
- Correspondence: ; Tel.: +82-31-219-5196; Fax: +82-31-219-5154
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4
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Mahood T, Pascoe CD, Karakach TK, Jha A, Basu S, Ezzati P, Spicer V, Mookherjee N, Halayko AJ. Integrating Proteomes for Lung Tissues and Lavage Reveals Pathways That Link Responses in Allergen-Challenged Mice. ACS OMEGA 2021; 6:1171-1189. [PMID: 33490776 PMCID: PMC7818314 DOI: 10.1021/acsomega.0c04269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
To capture interplay between biological pathways, we analyzed the proteome from matched lung tissues and bronchoalveolar lavage fluid (BALF) of individual allergen-naïve and house dust mite (HDM)-challenged BALB/c mice, a model of allergic asthma. Unbiased label-free liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis quantified 2675 proteins from tissues and BALF of allergen-naïve and HDM-exposed mice. In comparing the four datasets, we found significantly greater diversity in proteins between lung tissues and BALF than in the changes induced by HDM challenge. The biological pathways enriched after allergen exposure were compartment-dependent. Lung tissues featured innate immune responses and oxidative stress, while BALF most strongly revealed changes in metabolism. We combined lung tissues and BALF proteomes, which principally highlighted oxidation reduction (redox) pathways, a finding influenced chiefly by the lung tissue dataset. Integrating lung and BALF proteomes also uncovered new proteins and biological pathways that may mediate lung tissue and BALF interactions after allergen challenge, for example, B-cell receptor signaling. We demonstrate that enhanced insight is fostered when different biological compartments from the lung are investigated in parallel. Integration of proteomes from lung tissues and BALF compartments reveals new information about protein networks in response to environmental challenge and interaction between intracellular and extracellular processes.
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Affiliation(s)
- Thomas
H. Mahood
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Christopher D. Pascoe
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Tobias K. Karakach
- Bioinformatics
Core Laboratory, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E
3P4, Canada
| | - Aruni Jha
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Sujata Basu
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Peyman Ezzati
- Manitoba
Centre for Proteomics and Systems Biology, Department of Internal
Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Victor Spicer
- Manitoba
Centre for Proteomics and Systems Biology, Department of Internal
Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Neeloffer Mookherjee
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Manitoba
Centre for Proteomics and Systems Biology, Department of Internal
Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Immunology, University of Manitoba, Winnipeg, Manitoba R3E 0T5, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Andrew J. Halayko
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
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5
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Nieto‐Fontarigo JJ, González‐Barcala FJ, Andrade‐Bulos LJ, San‐José ME, Cruz MJ, Valdés‐Cuadrado L, Crujeiras RM, Arias P, Salgado FJ. iTRAQ-based proteomic analysis reveals potential serum biomarkers of allergic and nonallergic asthma. Allergy 2020; 75:3171-3183. [PMID: 32424932 DOI: 10.1111/all.14406] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/16/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Asthma is heterogeneous disease with different phenotypes, endotypes and severities. Definition of these subgroups requires the identification of biomarkers in biological samples, and serum proteomics is a useful and minimally invasive method for this purpose. Therefore, the aim of this study was to detect serum proteins whose abundance is distinctively associated with different asthma phenotypes (allergic vs nonallergic) or severities. METHODS For each group of donors (32 healthy controls, 43 allergic rhinitis patients and 192 asthmatics with different phenotypes and severities), we generated two pools of sera that were analysed by a shotgun MS approach based on combinatorial peptide ligand libraries and iTRAQ-LC-MS/MS. RESULTS MS analyses identified 18 proteins with a differential abundance. Functional/network study of these proteins identified key processes for asthma pathogenesis, such as complement activation, extracellular matrix organization, platelet activation and degranulation, or post-translational protein phosphorylation. Furthermore, our results highlighted an enrichment of the "Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)" route in allergic asthma and the lectin pathway of complement activation in nonallergic asthma. Thus, several proteins (eg IGFALS, HSPG2, FCN2 or MASP1) displayed a differential abundance between the different groups of donors. Particularly, our results revealed IGFALS as a useful biomarker for moderate-severe allergic asthma. CONCLUSION Our data suggest a set of serum biomarkers, especially IGFALS, capable of differentiating allergic from nonallergic asthma. These proteins reveal different pathophysiological mechanisms and may be useful in the future for diagnosis, prognosis or targeted therapy purposes.
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Affiliation(s)
- Juan José Nieto‐Fontarigo
- Department of Biochemistry and Molecular Biology Faculty of Biology‐Biological Research Centre (CIBUS) Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - Francisco Javier González‐Barcala
- Department of Medicine Universidade de Santiago de Compostela Santiago de Compostela Spain
- Department of Respiratory Medicine University Hospital of Santiago de Compostela Santiago de Compostela Spain
- Health Research Institute of Santiago de Compostela (IDIS) Santiago de Compostela Spain
- Spanish Biomedical Research Networking Centre‐CIBERES Madrid Spain
| | - Luis Juan Andrade‐Bulos
- Department of Biochemistry and Molecular Biology Faculty of Biology‐Biological Research Centre (CIBUS) Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - María Esther San‐José
- Clinical Analysis Service University Hospital of Santiago de Compostela Santiago de Compostela Spain
| | - María Jesús Cruz
- Spanish Biomedical Research Networking Centre‐CIBERES Madrid Spain
- Department of Respiratory Medicine‐Hospital Vall d'Hebron Universitat Autònoma de Barcelona Barcelona Spain
| | - Luis Valdés‐Cuadrado
- Department of Medicine Universidade de Santiago de Compostela Santiago de Compostela Spain
- Department of Respiratory Medicine University Hospital of Santiago de Compostela Santiago de Compostela Spain
- Health Research Institute of Santiago de Compostela (IDIS) Santiago de Compostela Spain
| | - Rosa María Crujeiras
- Department of Statistics, Mathematical Analysis and Optimization Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - Pilar Arias
- Department of Biochemistry and Molecular Biology Faculty of Biology‐Biological Research Centre (CIBUS) Universidade de Santiago de Compostela Santiago de Compostela Spain
| | - Francisco Javier Salgado
- Department of Biochemistry and Molecular Biology Faculty of Biology‐Biological Research Centre (CIBUS) Universidade de Santiago de Compostela Santiago de Compostela Spain
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6
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Insights into glucocorticoid responses derived from omics studies. Pharmacol Ther 2020; 218:107674. [PMID: 32910934 DOI: 10.1016/j.pharmthera.2020.107674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/20/2020] [Indexed: 12/26/2022]
Abstract
Glucocorticoid drugs are commonly used in the treatment of several conditions, including autoimmune diseases, asthma and cancer. Despite their widespread use and knowledge of biological pathways via which they act, much remains to be learned about the cell type-specific mechanisms of glucocorticoid action and the reasons why patients respond differently to them. In recent years, human and in vitro studies have addressed these questions with genomics, transcriptomics and other omics approaches. Here, we summarize key insights derived from omics studies of glucocorticoid response, and we identify existing knowledge gaps related to mechanisms of glucocorticoid action that future studies can address.
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7
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Cao Y, Xu S, Kong W, Cai H, Xu Y. Identification and validation of differentially expressed proteins in serum of CSU patients with different duration of wheals using an iTRAQ labeling, 2D-LC-MS/MS. Exp Ther Med 2018; 16:4527-4536. [PMID: 30542401 PMCID: PMC6257644 DOI: 10.3892/etm.2018.6818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/14/2018] [Indexed: 11/28/2022] Open
Abstract
Chronic spontaneous urticaria (CSU) is one of the most common types of chronic urticaria (CU), with symptoms that recur easily, migrate and are refractory. It is unclear whether association between the differentiation of protein expression levels in the serum of CSU patients and the different duration of wheals exists. In the present study the samples were divided according to the duration of the wheals into group A (wheal duration <2 h) and group B (wheal duration 12–24 h). Differentially expressed proteins in sera of CSU patients with different durations of wheals were identified and validated with isobaric tags for relative and absolute quantitation (iTRAQ) in combination with two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC-MS/MS). Three hundred and seventy CSU serum-related proteins were initially identified. Among these proteins, ~30 had significant differences between the groups. According to the classification of biological functions and upregulated/downregulated values, serum amyloid A (SAA), CFL1, TPM4 and monocyte differentiation antigen (CD14) were chosen and validated by enzyme-linked immunosorbent assay (ELISA). The expression levels of CD14 in sera were not significantly different among the groups. SAA, CFL1 and TPM4 were associated with the wheal duration in CSU patients and therefore could be considered as new potential inflammatory biomarkers associated with CSU.
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Affiliation(s)
- Yanyun Cao
- Department of Dermatology, Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Shunming Xu
- Department of Dermatology, Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Wei Kong
- Department of Dermatology, Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Haibin Cai
- Department of Dermatology, Pudong New Area People's Hospital, Shanghai 201299, P.R. China
| | - Yang Xu
- Department of Dermatology, Pudong New Area People's Hospital, Shanghai 201299, P.R. China
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8
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Norman KC, Moore BB, Arnold KB, O’Dwyer DN. Proteomics: Clinical and research applications in respiratory diseases. Respirology 2018; 23:993-1003. [PMID: 30105802 PMCID: PMC6234509 DOI: 10.1111/resp.13383] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/05/2018] [Accepted: 07/19/2018] [Indexed: 12/27/2022]
Abstract
The proteome is the study of the protein content of a definable component of an organism in biology. However, the tissue-specific expression of proteins and the varied post-translational modifications, splice variants and protein-protein complexes that may form, make the study of protein a challenging yet vital tool in answering many of the unanswered questions in medicine and biology to date. Indeed, the spatial, temporal and functional composition of proteins in the human body has proven difficult to elucidate for many years. Given the effect of microRNA and epigenetic regulation on silencing and enhancing gene transcription, the study of protein arguably provides more accurate information on homeostasis and perturbation in health and disease. There have been significant advances in the field of proteomics in recent years, with new technologies and platforms available to the research community. In this review, we briefly discuss some of these new technologies and developments in the context of respiratory disease. We also discuss the types of data science approaches to analyses and interpretation of the large volumes of data generated in proteomic studies. We discuss the application of these technologies with regard to respiratory disease and highlight the potential for proteomics in generating major advances in the understanding of respiratory pathophysiology into the future.
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Affiliation(s)
- Katy C. Norman
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Bethany B. Moore
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, USA
| | - Kelly B. Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - David N. O’Dwyer
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, USA
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9
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Towards precision medicine in severe asthma: Treatment algorithms based on treatable traits. Respir Med 2018; 142:15-22. [PMID: 30170796 DOI: 10.1016/j.rmed.2018.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 11/23/2022]
Abstract
Asthma is a common disease, and although its clinical manifestations may be similar among patients, recent research discoveries have shown that it consists of several distinct clinical clusters or phenotypes, each with different underlying molecular pathways yielding different treatment responses. Based on these observations, an alternative approach - known as 'precision medicine' - has been proposed for the management of patients with severe asthma. Precision medicine advocates identification of treatable traits, linking them to therapeutic approaches targeting genetic, immunological, environmental, and/or lifestyle factors in individual patients. The main "goal" of this personalised approach is to enable choosing a treatment which will be more likely to produce a beneficial response in the individual patient rather than a 'one size fits all' approach. The aim of the present review is to discuss different ways of phenotyping asthma and to provide a rationale for treatment algorithms based on principles of precision medicine.
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10
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Galeone C, Scelfo C, Bertolini F, Caminati M, Ruggiero P, Facciolongo N, Menzella F. Precision Medicine in Targeted Therapies for Severe Asthma: Is There Any Place for "Omics" Technology? BIOMED RESEARCH INTERNATIONAL 2018; 2018:4617565. [PMID: 29992143 PMCID: PMC6016214 DOI: 10.1155/2018/4617565] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/23/2018] [Accepted: 05/17/2018] [Indexed: 12/28/2022]
Abstract
According to the current guidelines, severe asthma still represents a controversial topic in terms of definition and management. The introduction of novel biological therapies as a treatment option for severe asthmatic patients paved the way to a personalized approach, which aims at matching the appropriate therapy with the different asthma phenotypes. Traditional asthma phenotypes have been decomposing by an increasing number of asthma subclasses based on functional and physiopathological mechanisms. This is possible thanks to the development and application of different omics technologies. The new asthma classification patterns, particularly concerning severe asthma, include an increasing number of endotypes that have been identified using new omics technologies. The identification of endotypes provides new opportunities for the management of asthma symptoms, but this implies that biological therapies which target inflammatory mediators in the frame of specific patterns of inflammation should be developed. However, the pathway leading to a precision approach in asthma treatment is still at its beginning. The aim of this review is providing a synthetic overview of the current asthma management, with a particular focus on severe asthma, in the light of phenotype and endotype approach, and summarizing the current knowledge about "omics" science and their therapeutic relevance in the field of bronchial asthma.
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Affiliation(s)
- Carla Galeone
- Department of Medical Specialties, Pneumology Unit, Arcispedale Santa Maria Nuova, Azienda USL di Reggio Emilia-IRCCS, Viale Amendola 2, 42122 Reggio Emilia, Italy
| | - Chiara Scelfo
- Department of Medical Specialties, Pneumology Unit, Arcispedale Santa Maria Nuova, Azienda USL di Reggio Emilia-IRCCS, Viale Amendola 2, 42122 Reggio Emilia, Italy
| | - Francesca Bertolini
- Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Marco Caminati
- Asthma Center and Allergy Unit, Verona University Hospital, Piazzale L.A. Scuro, 37134 Verona, Italy
| | - Patrizia Ruggiero
- Department of Medical Specialties, Pneumology Unit, Arcispedale Santa Maria Nuova, Azienda USL di Reggio Emilia-IRCCS, Viale Amendola 2, 42122 Reggio Emilia, Italy
| | - Nicola Facciolongo
- Department of Medical Specialties, Pneumology Unit, Arcispedale Santa Maria Nuova, Azienda USL di Reggio Emilia-IRCCS, Viale Amendola 2, 42122 Reggio Emilia, Italy
| | - Francesco Menzella
- Department of Medical Specialties, Pneumology Unit, Arcispedale Santa Maria Nuova, Azienda USL di Reggio Emilia-IRCCS, Viale Amendola 2, 42122 Reggio Emilia, Italy
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11
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Mazi AR, Arzuman AS, Gurel B, Sahin B, Tuzuner MB, Ozansoy M, Baykal AT. Neonatal Neurodegeneration in Alzheimer's Disease Transgenic Mouse Model. J Alzheimers Dis Rep 2018; 2:79-91. [PMID: 30480251 PMCID: PMC6159732 DOI: 10.3233/adr-170049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive disorder characterized by a variety of molecular pathologies causing cortical dementia with a prominent memory deficit. Formation of the pathology, which begins decades before the diagnosis of the disease, is highly correlated with the clinical symptoms. Several proteomics studies were performed using animal models to monitor the alterations of the brain tissue proteome at different stages of AD. However, proteome changes in the brain regions of newborn transgenic mouse model have not been investigated yet. To this end, we analyzed protein expression alterations in cortex, hippocampus and cerebellum of transgenic mice carrying five familial AD mutations (5XFAD) at neonatal day-1. Our results indicate a remarkable difference in protein expression profile of newborn 5XFAD brain with region specific variations. Additionally, the proteins, which show similar expression alteration pattern in postmortem human AD brains, were determined. Bioinformatics analysis showed that the molecular alterations were mostly related to the cell morphology, cellular assembly and organization, and neuroinflammation. Moreover, morphological analysis revealed that there is an increase in neurite number of 5XFAD mouse neurons in vitro. We suggest that, molecular alterations in the AD brain exist even at birth, and perhaps the disease is silenced until older ages when the brain becomes vulnerable.
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Affiliation(s)
- Aise Rumeysa Mazi
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Aysegul Sumeyye Arzuman
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Busra Gurel
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Betul Sahin
- Acibadem Labmed R&D Laboratory, Istanbul, Turkey
| | | | - Mehmet Ozansoy
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Acibadem Labmed R&D Laboratory, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
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12
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Svenningsen S, Nair P. Asthma Endotypes and an Overview of Targeted Therapy for Asthma. Front Med (Lausanne) 2017; 4:158. [PMID: 29018800 PMCID: PMC5622943 DOI: 10.3389/fmed.2017.00158] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/12/2017] [Indexed: 12/04/2022] Open
Abstract
Guidelines for the management of severe asthma do not emphasize the measurement of the inflammatory component of airway disease to indicate appropriate treatments or to monitor response to treatment. Inflammation is a central component of asthma and contributes to symptoms, physiological, and structural abnormalities. It can be assessed by a number of endotyping strategies based on “omics” technology such as proteomics, transcriptomics, and metabolomics. It can also be assessed using simple cellular responses by quantitative cytometry in sputum. Bronchitis may be eosinophilic, neutrophilic, mixed-granulocytic, or paucigranulocytic (eosinophils and neutrophils not elevated). Eosinophilic bronchitis is usually a Type 2 (T2)-driven process and therefore a sputum eosinophilia of greater than 3% usually indicates a response to treatment with corticosteroids or novel therapies directed against T2 cytokines such as IL-4, IL-5, and IL-13. Neutrophilic bronchitis represents a non-T2-driven disease, which is generally a predictor of response to antibiotics and may be a predictor to therapies targeted at pathways that lead to neutrophil recruitment such as TNF, IL-1, IL-6, IL-8, IL-23, and IL-17. Paucigranulocytic disease may not warrant anti-inflammatory therapy. These patients, whose symptoms may be driven largely by airway hyper-responsiveness may benefit from smooth muscle-directed therapies such as bronchial thermoplasty or mast-cell directed therapies. This review will briefly summarize the current knowledge regarding “omics-based signatures” and cellular endotyping of severe asthma and give an overview of segmentation of asthma therapeutics guided by the endotype.
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Affiliation(s)
| | - Parameswaran Nair
- Department of Medicine, McMaster University, Hamilton, ON, Canada.,St Joseph's Healthcare, Hamilton, ON, Canada
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13
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Diao W, Shen N, Du Y, Sun X, Liu B, Xu M, He B. Identification of thyroxine-binding globulin as a candidate plasma marker of chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis 2017; 12:1549-1564. [PMID: 28579773 PMCID: PMC5448702 DOI: 10.2147/copd.s137806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Biomarkers for the management of chronic obstructive pulmonary disease (COPD) are limited. The aim of this study was to explore new plasma biomarkers in patients with COPD. Thyroxine-binding globulin (THBG) was initially identified by proteomics in a discovery panel and subsequently verified by enzyme-linked immunosorbent assay in another verification panel with a 1-year follow-up. THBG levels were elevated in patients with COPD (9.2±2.3 μg/mL) compared to those of the controls (6.6±2.0 μg/mL). Receiver operating characteristic curves suggested that THBG was able to slightly differentiate between patients with COPD and controls (area under the curve [AUC]: 0.814) and performed better if combined with fibrinogen (AUC: 0.858). THBG was more capable of distinguishing Global Initiative for Obstructive Lung Disease stages I–III and IV (AUC: 0.851) compared with fibrinogen (AUC 0.582). THBG levels were negatively associated with predicted percentage forced expiratory volume in 1 s and positively related to predicted percentage residual volume, RV/percentage total lung capacity, and percentage low-attenuation area. COPD patients with higher baseline THBG levels had a greater risk of acute exacerbation (AE) than those with lower THBG levels (P=0.014, by Kaplan–Meier curve; hazard ratio: 4.229, by Cox proportional hazards model). In summary, THBG is a potential plasma biomarker of COPD and can assist in the management of stable stage and AEs in COPD patients.
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Affiliation(s)
| | | | | | | | | | - Ming Xu
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital.,Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, People's Republic of China
| | - Bei He
- Department of Respiratory Medicine
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14
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Zhang C, Abudula A, Awuti M, Wang H, Aihemaiti X, Tusung T, Sulaiman X, Upur H. Plasma proteins as potential targets of abnormal Savda syndrome in asthma patients treated with unique Uighur prescription. Exp Ther Med 2017; 14:267-275. [PMID: 28672924 PMCID: PMC5488641 DOI: 10.3892/etm.2017.4500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/02/2017] [Indexed: 12/18/2022] Open
Abstract
The therapeutic effect of Uighur prescription on abnormal Savda in asthma patients was evaluated using plasma proteomics in order to elucidate the biological mechanism and identify potential therapeutic targets of abnormal Savda. In the present study, 40 asthma patients with abnormal Savda including abnormal Savda Munziq and Savda Mushil were enrolled and treated with Uighur prescription. The effect of Uighur prescription on protein expression and potential targets was investigated by isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics and bioinformatics analysis. Expression of candidate proteins was verified by an enzyme-linked immunosorbent assay. Following treatment with the Uighur prescription, 22 proteins were differentially expressed in the plasma of patients with asthma and abnormal Savda. The majority of these proteins were localized in intermediate filaments and the cytoskeleton and acted as antioxidant enzymes and binding proteins. Furthermore, they participated in the defense and inflammatory response, and the response to oxidative stress and wound healing. Peroxiredoxin 2 and carboxypeptidase B2 expression was significantly upregulated, whereas S100A7 was considerably downregulated in the whole plasma of patients (all P<0.05) in accordance with the iTRAQ proteomics data. Uighur prescription of abnormal Savda may affect the whole regulatory network of protein expression that is altered following the development of abnormal Savda in patients with asthma.
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Affiliation(s)
- Canhua Zhang
- School of Uyghur Medicine, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Abulizi Abudula
- Key Laboratory of High-Incident Diseases in Uyghur Ethnic Population Supported by The Chinese Ministry of Education, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Maliyegu Awuti
- Department of Respiratory Pneumology, First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Huiwu Wang
- Department of Pulmonary Function, First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Xiaimuxikamaier Aihemaiti
- Department of Respiratory Pneumology, First Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Turghun Tusung
- School of Uyghur Medicine, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | | | - Halmurat Upur
- Key Laboratory of High-Incident Diseases in Uyghur Ethnic Population Supported by The Chinese Ministry of Education, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
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15
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Herath TDK, Darveau RP, Seneviratne CJ, Wang CY, Wang Y, Jin L. Heterogeneous Porphyromonas gingivalis LPS modulates immuno-inflammatory response, antioxidant defense and cytoskeletal dynamics in human gingival fibroblasts. Sci Rep 2016; 6:29829. [PMID: 27538450 PMCID: PMC4990928 DOI: 10.1038/srep29829] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022] Open
Abstract
Periodontal (gum) disease is a highly prevalent infection and inflammation accounting for the majority of tooth loss in adult population worldwide. Porphyromonas gingivalis is a keystone periodontal pathogen and its lipopolysaccharide (PgLPS) acts as a major virulence attribute to the disease. Herein, we deciphered the overall host response of human gingival fibroblasts (HGFs) to two featured isoforms of tetra-acylated PgLPS1435/1449 and penta-acylated PgLPS1690 with reference to E. coli LPS through quantitative proteomics. This study unraveled differentially expressed novel biomarkers of immuno-inflammatory response, antioxidant defense and cytoskeletal dynamics in HGFs. PgLPS1690 greatly upregulated inflammatory proteins (e.g. cyclophilin, inducible nitric oxide synthase, annexins, galectin, cathepsins and heat shock proteins), whereas the anti-inflammatory proteins (e.g. Annexin A2 and Annexin A6) were significantly upregulated by PgLPS1435/1449. Interestingly, the antioxidants proteins such as mitochondrial manganese-containing superoxide dismutase and peroxiredoxin 5 were only upregulated by PgLPS1690. The cytoskeletal rearrangement-related proteins like myosin were differentially regulated by these PgLPS isoforms. The present study gives new insight into the biological properties of P. gingivalis LPS lipid A moiety that could critically modulate immuno-inflammatory response, antioxidant defense and cytoskeletal dynamics in HGFs, and thereby enhances our understanding of periodontal pathogenesis.
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Affiliation(s)
- Thanuja D K Herath
- National Dental Centre Singapore, Singapore.,Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | | | | | - Cun-Yu Wang
- School of Dentistry, University of California Los Angeles, Los Angeles, USA
| | - Yu Wang
- Department of Pharmacology &Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lijian Jin
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
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Bagnasco D, Ferrando M, Bernardi S, Passalacqua G, Canonica GW. The path to personalized medicine in asthma. Expert Rev Respir Med 2016; 10:957-65. [PMID: 27399975 DOI: 10.1080/17476348.2016.1205490] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Asthma is a common respiratory disorder, since about 10% of the population suffer from this disease, and up to 10% have a severe form. Recent findings have allowed a greater and deeper understanding of the pathophysiological mechanisms, distinguishing two groups of patients according to the prevalent cellular population that drives the inflammatory process, and consequentially, to intervene on different cellular targets. AREAS COVERED Currently, several biological drugs directly interfering with these pathophysiological mechanisms (namely IgE, IL-4, IL-5, IL-13, and IL-17) are under investigation. Expert commentary: With the elucidation of mechanisms, new-targeted drugs have been developed. Asthma therapy is changing from a 'one size fits all' therapy to a 'precision medicine' model, where we may prescribe the most appropriate treatment for each patient. Moreover, in the near future, the possibility to act a 'sequential bio-combination therapy' can be envisaged, using different biological drugs in the same patient to act on different pathophysiological mechanisms.
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Affiliation(s)
- Diego Bagnasco
- a Allergy & Respiratory Diseases, DIMI, Department of Internal Medicine , University of Genoa, IRCCS AOU San Martino - IST , Genoa , Italy
| | - Matteo Ferrando
- a Allergy & Respiratory Diseases, DIMI, Department of Internal Medicine , University of Genoa, IRCCS AOU San Martino - IST , Genoa , Italy
| | - Stefano Bernardi
- a Allergy & Respiratory Diseases, DIMI, Department of Internal Medicine , University of Genoa, IRCCS AOU San Martino - IST , Genoa , Italy
| | - Giovanni Passalacqua
- a Allergy & Respiratory Diseases, DIMI, Department of Internal Medicine , University of Genoa, IRCCS AOU San Martino - IST , Genoa , Italy
| | - Giorgio Walter Canonica
- a Allergy & Respiratory Diseases, DIMI, Department of Internal Medicine , University of Genoa, IRCCS AOU San Martino - IST , Genoa , Italy
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Developing a framework for assessing chemical respiratory sensitization: A workshop report. Regul Toxicol Pharmacol 2016; 80:295-309. [PMID: 27396307 DOI: 10.1016/j.yrtph.2016.06.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 12/29/2022]
Abstract
Respiratory tract sensitization can have significant acute and chronic health implications. While induction of respiratory sensitization is widely recognized for some chemicals, validated standard methods or frameworks for identifying and characterizing the hazard are not available. A workshop on assessment of respiratory sensitization was held to discuss the current state of science for identification and characterization of respiratory sensitizer hazard, identify information facilitating development of validated standard methods and frameworks, and consider the regulatory and practical risk management needs. Participants agreed on a predominant Th2 immunological mechanism and several steps in respiratory sensitization. Some overlapping cellular events in respiratory and skin sensitization are well understood, but full mechanism(s) remain unavailable. Progress on non-animal approaches to skin sensitization testing, ranging from in vitro systems, -omics, in silico profiling, and structural profiling were acknowledged. Addressing both induction and elicitation phases remains challenging. Participants identified lack of a unifying dose metric as increasing the difficulty of interpreting dosimetry across exposures. A number of research needs were identified, including an agreed list of respiratory sensitizers and other asthmagens, distinguishing between adverse effects from immune-mediated versus non-immunological mechanisms. A number of themes emerged from the discussion regarding future testing strategies, particularly the need for a tiered framework respiratory sensitizer assessment. These workshop present a basis for moving towards a weight-of-evidence assessment.
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18
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Increased serum VDBP as a risk predictor for steroid resistance in asthma patients. Respir Med 2016; 114:111-6. [PMID: 27109820 DOI: 10.1016/j.rmed.2016.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 01/23/2023]
Abstract
BACKGROUND Asthmatic symptoms usually can be controlled with corticosteroids, but partly asthmatic patients do not respond to corticosteroids, steroid resistance (SR) play a significant role in the poorly responding. However, no approach can accurately predict steroid responsiveness in asthma patients, so prediction of SR with noninvasive means has become a critical issue. OBJECTIVE The aim of this study was to evaluate the difference in serum proteomes between steroid-sensitive asthma (SSA) and steroid-resistant asthma (SRA) patients and identify potential biomarkers for the prediction of SR in asthma patients. METHODS We performed a proteomic approach of fluorescence-based difference gel electrophoresis (DIGE) and mass spectrometry to identify biomarkers in the serum obtained from SRA and SSA patients (n = 6 in each group). The interesting biomarker was further studied using western blot and enzyme-linked immunosorbent assays (ELISA). RESULTS Seven differentially expressed proteins between SSA and SRA group were identified. Among them, vitamin D-binding protein (VDBP) attracted our further attention as the greatest changed protein. Serum VDBP was significantly up-regulated in SRA group compared with SSA group, and the differential expression was confirmed with western blot analysis. The ELISA data showed the serum level of VDBP was significantly higher in SRA group than that in SSA and control group (496.50 ± 204.62 vs. 279.73 ± 163.65, 241.93 ± 98.58 μg/ml, respectively, p < 0.01). Correlation analysis indicated serum VDBP was positively correlated with neutrophils% and monocytes% (p < 0.05), but inversely correlate with serum 25OHD (p < 0.05). Regression analysis showed increased serum VDBP was a risk predictor of SRA, and serum 25OHD was an independent influential factor of serum VDBP. Using the receiver operating characteristic curve, we determined the area under the curve (AUC) of VDBP was 0.792, and the optimal serum cutoff value of VDBP was 355.8 μg/ml, which can discriminate SRA from asthma patients with 65.2% sensitivity and 83.7% specificity. CONCLUSIONS This study provides a novel overview of the difference in serum proteomes of SSA and SRA. We suppose serum VDBP may serve as a useful biomarker for predicting SR in asthma patients, and may participate in the pathogenesis of SRA.
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Personalized Medicine in Respiratory Disease: Role of Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 102:115-46. [PMID: 26827604 DOI: 10.1016/bs.apcsb.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Respiratory diseases affect humanity globally, with chronic lung diseases (e.g., asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, among others) and lung cancer causing extensive morbidity and mortality. These conditions are highly heterogeneous and require an early diagnosis. However, initial symptoms are nonspecific, and the clinical diagnosis is made late frequently. Over the last few years, personalized medicine has emerged as a medical care approach that uses novel technology aiming to personalize treatments according to the particular patient's medical needs. This review highlights the contributions of proteomics toward the understanding of personalized medicine in respiratory disease and its potential applications in the clinic.
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20
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Clinical phenotypes of asthma should link up with disease mechanisms. Curr Opin Allergy Clin Immunol 2015; 15:56-62. [PMID: 25504141 DOI: 10.1097/aci.0000000000000134] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Asthma is a common disease which presents in various clinical forms and levels of severity. The current 'one size fits all' approach to treatment is suboptimal. Using unbiased cluster analysis has identified several asthma phenotypes. Understanding the underlying mechanisms driving these clusters may lead to better patient-orientated medicines. RECENT FINDINGS Clustering was initially performed on clinical features only, but the addition of biomarkers that characterize sputum and blood cellular profiles has enabled the prediction of responses to targeted therapies. Clusters of severe asthma include those on high-dose corticosteroid treatment associated with severe airflow obstruction and those with discordance between symptoms and sputum eosinophilia. Sputum eosinophilia can predict therapeutic responses to T-helper type 2 cytokine blockade. Further molecular phenotyping or endotyping of asthma will be necessary to determine new treatment strategies. Low T-helper type 2 expression may be predictive of poor therapeutic response to inhaled corticosteroids, but much less is known about this type of asthma. SUMMARY Phenotype-driven treatment of asthma will be further boosted by the integration of genetic, transcriptomic and proteomic technologies to defining distinct severe asthma phenotypes and biomarkers of therapeutic responses. This will lead towards stratified medicine for asthma.
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Abstract
Asthma is a common disease with a complex pathophysiology. It can present in various clinical forms and with different levels of severity. Unbiased cluster analytic methods have unravelled several phenotypes in cohorts representative of the whole spectrum of severity. Clusters of severe asthma include those on high-dose corticosteroid treatment, often with both inhaled and oral treatment, usually associated with severe airflow obstruction. Phenotypes with concordance between symptoms and sputum eosinophilia have been reported, including an eosinophilic inflammation-predominant group with few symptoms and late-onset disease who have a high prevalence of rhinosinusitis, aspirin sensitivity, and exacerbations. Sputum eosinophilia is also a biomarker that can predict therapeutic responses to antibody-based treatments to block the effects of the T-helper (Th)-2 cytokine, interleukin (IL)-5. Low Th2-expression has been predictive of poor therapeutic response to inhaled corticosteroid therapy. Current asthma schedules emphasise a step-up approach to treating asthma in relation to increasing severity, but, in more severe disease, phenotyping or endotyping of asthma will be necessary to determine new treatment strategies as severe asthma is recognized as being a particularly heterogeneous disease. Much less is known about 'non-eosinophilic' asthma. Phenotypic characterisation of corticosteroid insensitivity and chronic airflow obstruction of severe asthma is also needed. Phenotype-driven treatment of asthma will be further boosted by the advent of transcriptomic and proteomic technologies, with the application of systems biology or medicine approaches to defining phenotypes and biomarkers of disease and therapeutic response. This will pave the way towards personalized medicine and healthcare for asthma.
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Affiliation(s)
- Kian Fan Chung
- Experimental Studies, National Heart and Lung Institute, Imperial College London, Dovehouse St, London, SW3 6LY, UK,
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22
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Teran LM, Montes-Vizuet R, Li X, Franz T. Respiratory proteomics: from descriptive studies to personalized medicine. J Proteome Res 2014; 14:38-50. [PMID: 25382407 DOI: 10.1021/pr500935s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Respiratory diseases are highly prevalent and affect humankind worldwide, causing extensive morbidity and mortality with the environment playing an important role. Given the complex structure of the airways, sophisticated tools are required for early diagnosis; initial symptoms are nonspecific, and the clinical diagnosis is made frequently late. Over the past few years, proteomics has made high technological progress in mass-spectrometry-based protein identification and has allowed us to gain new insights into disease mechanisms and identify potential novel therapeutic targets. This review will highlight the contributions of proteomics toward the understanding of the respiratory proteome listing potential biomarkers and its potential application to the clinic. We also outline the contributions of proteomics to creating a personalized approach in respiratory medicine.
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Affiliation(s)
- Luis M Teran
- Instituto Nacional de Enfermedades Respiratorias , Calz. de Tlalpan 4502, Distrito Federal 14080, Mexico
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23
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Rossi R, De Palma A, Benazzi L, Riccio AM, Canonica GW, Mauri P. Biomarker discovery in asthma and COPD by proteomic approaches. Proteomics Clin Appl 2014; 8:901-15. [PMID: 25186471 DOI: 10.1002/prca.201300108] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 07/01/2014] [Accepted: 09/01/2014] [Indexed: 11/07/2022]
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are multifactorial respiratory diseases, characterized by reversible and irreversible airway obstruction, respectively. Even if the primary causes of these diseases remain unknown, inflammation is a central feature that leads to progressive and permanent pulmonary tissue damage (airway remodeling) up to the total loss of lung function. Therefore, the elucidation of the inflammation mechanisms and the characterization of the biological pathways, involved in asthma and COPD pathogenesis, are relevant in finding new possible diagnostic/prognostic biomarkers and for the validation of new drug targets. In this context, current advances in proteomic approaches, especially those based on MS, provide new tools to facilitate the discovery-driven studies of new biomarkers in respiratory diseases and improve the clinical reliability of the next generation of biomarkers for these diseases consisting of multiple phenotypes. This review will report an overview of the current proteomic methods applied to the discovery of candidate biomarkers for asthma and COPD, giving a special emphasis to emerging MS-based techniques.
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Affiliation(s)
- Rossana Rossi
- Institute for Biomedical Technologies (ITB-CNR), Proteomics and Metabolomics Unit, Segrate, MI, Italy
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24
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Abstract
PURPOSE OF REVIEW The purpose of this review is to discuss the present systems biology approach to asthma and how it is helping to define asthma subtypes. Although the general concept of systems biology will be discussed, the article will focus on recent developments in the field related to asthma. RECENT FINDINGS The most recent work in systems biology and asthma has occurred in the area of genomics (e.g., pharmacogenomics and gene-environment interactions), protein interaction networks [e.g., interleukin (IL)-33/IL-1 receptor-like 1 signaling], cluster analysis of asthma patients (e.g., application of severe asthma research program clusters to a general urban asthma population), and multiscale approaches to asthma encompassing data from the molecule to whole organ (e.g., modeling of airways hyperresponsiveness). SUMMARY The results of recent work in this area have led to new insight into gene-cytokine and protein-protein networks involved in asthma, a better determination of key clinical factors associated with asthma subtypes, and the beginning of sophisticated multiscale approaches to modeling, understanding and predicting the behavior of the asthmatic lung.
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Wiktorowicz JE, Jamaluddin M. Proteomic analysis of the asthmatic airway. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 795:221-32. [PMID: 24162912 DOI: 10.1007/978-1-4614-8603-9_14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Proteomic investigations in general utilize varied technologies for sample preparation, separations, quantification, protein identification, and biological rationalization. Their applications range from pure discovery and mechanistic studies to biomarker discovery/verification/validation. In each specific case, the analytical strategy to be implemented is tailored to the type of sample that serves as the target of the investigations. Proteomic investigations take into consideration sample complexity, the cellular heterogeneity (particularly from tissues), the potential dynamic range of the protein and peptide abundance within the sample, the likelihood of posttranslational modifications (PTM), and other important factors that might influence the final output of the study. We describe the sample types typically used for proteomic investigations into the biology of asthma and review the most recent related publications with special attention to those that deal with the unique airway samples such as bronchoalveolar lavage fluids (BALF), epithelial lining fluid and cells (ELF), induced sputum (IS), and exhaled breath condensate (EBC). Finally, we describe the newest proteomics approaches to sample preparation of the unique airway samples, BALF and IS.
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Affiliation(s)
- John E Wiktorowicz
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, 2.208A Basic Science Bldg, 301 University Blvd, Galveston, TX, 77555-0635, USA,
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Mo Y, Hou H, Li D, Liang Y, Chen D, Zhou Y. Mitochondrial protein targets of radiosensitisation by 1,8-dihydroxy-3-acetyl-6-methyl-9,10 anthraquinone on nasopharyngeal carcinoma cells. Eur J Pharmacol 2014; 738:133-41. [PMID: 24877689 DOI: 10.1016/j.ejphar.2014.05.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/01/2014] [Accepted: 05/07/2014] [Indexed: 12/11/2022]
Abstract
In our preliminary study, 1,8-dihydroxy-3-acetyl-6-methyl-9,10 anthraquinone (GXHSWAQ-1), synthesised according to the basic structure of emodin, exhibited a 1.58-fold radiosensitisation on nasopharyngeal carcinoma CNE-1 cells. This study demonstrated that its radiosensitisation activity was achieved by altering the mitochondrial structure: swollen volume, fragmented crista, and decreasing transmembrane potential (P<0.01). Using isobaric tag for relative and absolute quantitation (iTRAQ) technology, 1396 proteins were identified, and the differentially expressed proteins were involved in metabolism, cell proliferation, angiogenesis, DNA repair process according to the biological process clustering results. Bioinformatic analysis showed that CDH1, RAC1, CDC42 proteins might be mostly mitochondrial targets in the radiosensitisation process. Western blotting analyses verified the differential expression of these proteins.
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Affiliation(s)
- Yuanyuan Mo
- College of Pharmacy, Guangxi Medical University, Nanning 530021 China
| | - Huaxin Hou
- College of Pharmacy, Guangxi Medical University, Nanning 530021 China.
| | - Danrong Li
- Guangxi Institute for Cancer Research, Nanning 530021, China.
| | - Yan Liang
- College of Pharmacy, Guangxi Medical University, Nanning 530021 China
| | - Donglian Chen
- College of Pharmacy, Guangxi Medical University, Nanning 530021 China
| | - Yi Zhou
- Guangxi Institute for Cancer Research, Nanning 530021, China
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Chung KF, Adcock IM. How variability in clinical phenotypes should guide research into disease mechanisms in asthma. Ann Am Thorac Soc 2013; 10 Suppl:S109-17. [PMID: 24313760 PMCID: PMC3960989 DOI: 10.1513/annalsats.201304-087aw] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 06/14/2013] [Indexed: 12/15/2022] Open
Abstract
Asthma is increasingly being considered as a collection of different phenotypes that present with intermittent wheezing. Unbiased approaches to classifying asthma have led to the identification of distinct phenotypes based on age of onset of disease, atopic state, disease severity or activity, degree of chronic airflow obstruction, and sputum eosinophilia. Linking phenotypes to known disease mechanism is likely to be more fruitful in determining the potential targets necessary for successful therapies of specific endotypes. A "Th2-high expression" signature from the epithelium of patients with asthma identifies a subset of patients with high eosinophilia and good therapeutic responsiveness to corticosteroids. Other characteristic traits of asthma include noneosinophilic asthma, corticosteroid insensitivity, obesity-associated, and exacerbation-prone. Further progress into asthma mechanisms will be driven by unbiased data integration of multiscale data sets from omics technologies with those phenotypic characteristics and by using mathematical modeling. This will lead to the discovery of new pathways and their integration into endotypes and also set up further hypothesis-driven research. Continued iteration through experimentation or modeling will be needed to refine the phenotypes that relate to outcomes and also delineate specific treatments for specific phenotypes.
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Affiliation(s)
- Kian Fan Chung
- Airways Disease, National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
| | - Ian M. Adcock
- Biomedical Research Unit, Royal Brompton Hospital, London, United Kingdom
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Abstract
Asthma has a high prevalence worldwide, and contributes significantly to the socioeconomic burden. According to a classical paradigm, asthma symptoms are attributable to an allergic, Th2-driven airway inflammation that causes airway hyperresponsiveness and results in reversible airway obstruction. Diagnosis and therapy are based mainly on these pathophysiologic concepts. However, these have increasingly been challenged by findings of recent studies, and the frequently observed failure in controlling asthma symptoms. Important recent findings are the protective "farm effect" in children, the possible prenatal mechanisms of this protection, the recognition of many different asthma phenotypes in children and adults, and the partly disappointing clinical effects of new targeted therapeutic approaches. Systems biology approaches may lead to a more comprehensive view of asthma pathophysiology and a higher success rate of new therapies. Systems biology integrates clinical and experimental data by means of bioinformatics and mathematical modeling. In general, the "-omics" approach, and the "mathematical modeling" approach can be described. Recently, several consortia have been attempting to bring together clinical and molecular data from large asthma cohorts, using novel experimental setups, biostatistics, bioinformatics, and mathematical modeling. This "systems medicine" approach to asthma will help address the different asthma phenotypes with adequate therapy and possibly preventive strategies.
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Singh A, Cohen Freue GV, Oosthuizen JL, Kam SHY, Ruan J, Takhar MK, Gauvreau GM, O'Byrne PM, Fitzgerald JM, Boulet LP, Borchers CH, Tebbutt SJ. Plasma proteomics can discriminate isolated early from dual responses in asthmatic individuals undergoing an allergen inhalation challenge. Proteomics Clin Appl 2013; 6:476-85. [PMID: 22930592 DOI: 10.1002/prca.201200013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
PURPOSE This proteomics study was designed to determine the utility of iTRAQ MALDI-TOF/TOF technology to compare plasma samples from carefully phenotyped mild, atopic asthma subjects undergoing allergen inhalation challenge. EXPERIMENTAL DESIGN Eight adult subjects with mild, allergic asthma (four early responders (ERs) and four dual responders (DRs)) participated in the allergen inhalation challenge. Blood samples were collected prior to and 2 h after the inhalation challenge. Sixteen plasma samples (two per subject), technical replicates, and pooled controls were analyzed using iTRAQ. Technical validation was performed using LC-MRM/MS. Moderated robust regression was used to determine differentially expressed proteins. RESULTS Although this study did not show significant differences between pre- and post-challenge samples, discriminant analysis indicated that certain proteins responded differentially to allergen challenge with respect to responder type. At pre-challenge, fibronectin was significantly elevated in DRs compared to ERs and remained significant in the multiple reaction monitoring validation. CONCLUSIONS AND CLINICAL RELEVANCE This proof of principle demonstration has shown that iTRAQ can uncover differences in the human plasma proteome between two endotypes of asthma and merits further application of iTRAQ to larger cohorts of asthma and other respiratory diseases.
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Affiliation(s)
- Amrit Singh
- James Hogg Research Centre, St. Paul's Hospital, University of British Columbia, Vancouver, Canada
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30
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Pillai RR, Divekar R, Brasier A, Bhavnani S, Calhoun WJ. Strategies for molecular classification of asthma using bipartite network analysis of cytokine expression. Curr Allergy Asthma Rep 2013; 12:388-95. [PMID: 22777399 DOI: 10.1007/s11882-012-0279-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Asthma is a chronic inflammatory disease of the airways that leads to various degrees of recurrent respiratory symptoms affecting patients globally. Specific subgroups of asthma patients have severe disease leading to increased healthcare costs and socioeconomic burden. Despite the overwhelming prevalence of the asthma, there are limitations in predicting response to therapy and identifying patients who are at increased risk of morbidity. This syndrome presents with common clinical signs and symptoms; however, awareness of subgroups of asthma patients with distinct characteristics has surfaced in recent years. Investigators attempt to describe the phenotypes of asthma to ultimately assist with diagnostic and therapeutic applications. Approaches to asthma phenotyping are multifold; however, it can be partitioned into 2 essential groups, clinical phenotyping and molecular phenotyping. Innovative techniques such as bipartite network analysis and visual analytics introduce a new dimension of data analysis to identify underlying mechanistic pathways.
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Affiliation(s)
- Regina R Pillai
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Texas Medical Branch, 5.140 John Sealy Annex, 301 University Blvd, Galveston, TX 77555-0561, USA.
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31
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O'Neil SE, Lundbäck B, Lötvall J. Proteomics in asthma and COPD phenotypes and endotypes for biomarker discovery and improved understanding of disease entities. J Proteomics 2011; 75:192-201. [PMID: 22037230 DOI: 10.1016/j.jprot.2011.10.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 10/10/2011] [Accepted: 10/12/2011] [Indexed: 11/17/2022]
Abstract
The application of proteomics to respiratory diseases, such as asthma and COPD, has been limited compared to other fields, like cancer. Both asthma and COPD are recognised to be multi-factorial and complex diseases, both consisting of clusters of multiple disease phenotypes. The complexity of these diseases combined with the inaccessibility and invasiveness of disease relevant samples have provided a hurdle to the progress of respiratory proteomics. Advances in proteomic instrumentation and methodology have led to the possibility to identify proteomes in much smaller quantities of biological material. This review focuses on the efforts in respiratory proteomics in relation to asthma and COPD, and the importance of identifying subgroups of disease entities to establish appropriate biomarkers, and to enhance the understanding of underlying mechanisms in each subgroup. Careful phenotype characterisation of patient subpopulations is required to make improvement in the field of heterogeneous diseases such as asthma and COPD, and the clusters of phenotypes are likely to encompass subgroups of disease with distinct molecular mechanisms; endotypes. The utilisation of modern advanced proteomics in endotypes of asthma and COPD will likely contribute to the increased understanding of disease mechanisms, establishment of biomarkers for these endotypes and improved patient care.
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Affiliation(s)
- Serena E O'Neil
- Krefting Research Centre, Department of Internal Medicine, University of Gothenburg, Sweden.
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