1
|
The Role of Systems Biology in Deciphering Asthma Heterogeneity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101562. [PMID: 36294997 PMCID: PMC9605413 DOI: 10.3390/life12101562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
Asthma is one of the most common and lifelong and chronic inflammatory diseases characterized by inflammation, bronchial hyperresponsiveness, and airway obstruction episodes. It is a heterogeneous disease of varying and overlapping phenotypes with many confounding factors playing a role in disease susceptibility and management. Such multifactorial disorders will benefit from using systems biology as a strategy to elucidate molecular insights from complex, quantitative, massive clinical, and biological data that will help to understand the underlying disease mechanism, early detection, and treatment planning. Systems biology is an approach that uses the comprehensive understanding of living systems through bioinformatics, mathematical, and computational techniques to model diverse high-throughput molecular, cellular, and the physiologic profiling of healthy and diseased populations to define biological processes. The use of systems biology has helped understand and enrich our knowledge of asthma heterogeneity and molecular basis; however, such methods have their limitations. The translational benefits of these studies are few, and it is recommended to reanalyze the different studies and omics in conjugation with one another which may help understand the reasons for this variation and help overcome the limitations of understanding the heterogeneity in asthma pathology. In this review, we aim to show the different factors that play a role in asthma heterogeneity and how systems biology may aid in understanding and deciphering the molecular basis of asthma.
Collapse
|
2
|
Hachim MY, Elemam NM, Ramakrishnan RK, Salameh L, Olivenstein R, Hachim IY, Venkatachalam T, Mahboub B, Al Heialy S, Hamid Q, Hamoudi R. Derangement of cell cycle markers in peripheral blood mononuclear cells of asthmatic patients as a reliable biomarker for asthma control. Sci Rep 2021; 11:11873. [PMID: 34088958 PMCID: PMC8178351 DOI: 10.1038/s41598-021-91087-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
In asthma, most of the identified biomarkers pertain to the Th2 phenotype and no known biomarkers have been verified for severe asthmatics. Therefore, identifying biomarkers using the integrative phenotype-genotype approach in severe asthma is needed. The study aims to identify novel biomarkers as genes or pathways representing the core drivers in asthma development, progression to the severe form, resistance to therapy, and tissue remodeling regardless of the sample cells or tissues examined. Comprehensive reanalysis of publicly available transcriptomic data that later was validated in vitro, and locally recruited patients were used to decipher the molecular basis of asthma. Our in-silicoanalysis revealed a total of 10 genes (GPRC5A, SFN, ABCA1, KRT8, TOP2A, SERPINE1, ANLN, MKI67, NEK2, and RRM2) related to cell cycle and proliferation to be deranged in the severe asthmatic bronchial epithelium and fibroblasts compared to their healthy counterparts. In vitro, RT qPCR results showed that (SERPINE1 and RRM2) were upregulated in severe asthmatic bronchial epithelium and fibroblasts, (SFN, ABCA1, TOP2A, SERPINE1, MKI67, and NEK2) were upregulated in asthmatic bronchial epithelium while (GPRC5A and KRT8) were upregulated only in asthmatic bronchial fibroblasts. Furthermore, MKI76, RRM2, and TOP2A were upregulated in Th2 high epithelium while GPRC5A, SFN, ABCA1 were upregulated in the blood of asthmatic patients. SFN, ABCA1 were higher, while MKI67 was lower in severe asthmatic with wheeze compared to nonasthmatics with wheezes. SERPINE1 and GPRC5A were downregulated in the blood of eosinophilic asthmatics, while RRM2 was upregulated in an acute attack of asthma. Validation of the gene expression in PBMC of locally recruited asthma patients showed that SERPINE1, GPRC5A, SFN, ABCA1, MKI67, and RRM2 were downregulated in severe uncontrolled asthma. We have identified a set of biologically crucial genes to the homeostasis of the lung and in asthma development and progression. This study can help us further understand the complex interplay between the transcriptomic data and the external factors which may deviate our understanding of asthma heterogeneity.
Collapse
Affiliation(s)
- Mahmood Yaseen Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
| | - Noha Mousaad Elemam
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Rakhee K Ramakrishnan
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Laila Salameh
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Ibrahim Yaseen Hachim
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Thenmozhi Venkatachalam
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Meakins-Christie Laboratories, McGill University, Montreal, QC, Canada
| | - Qutayba Hamid
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Meakins-Christie Laboratories, McGill University, Montreal, QC, Canada
| | - Rifat Hamoudi
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Division of Surgery and Interventional Science, UCL, London, UK
| |
Collapse
|
3
|
Abstract
While asthma has a strong genetic component, our current ability to systematically understand and predict asthma risk remains low, despite over a hundred genetic associations. The reasons for this unfilled gap range from technical limitations of current approaches to fundamental deficiencies in the way we understand asthma. These are discussed in the context of genomic advances.
Collapse
Affiliation(s)
- Mayank Bansal
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mayank Garg
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| |
Collapse
|
4
|
Resolving Clinical Phenotypes into Endotypes in Allergy: Molecular and Omics Approaches. Clin Rev Allergy Immunol 2020; 60:200-219. [PMID: 32378146 DOI: 10.1007/s12016-020-08787-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allergic diseases are highly complex with respect to pathogenesis, inflammation, and response to treatment. Current efforts for allergic disease diagnosis have focused on clinical evidence as a binary outcome. Although outcome status based on clinical phenotypes (observable characteristics) is convenient and inexpensive to measure in large studies, it does not adequately provide insight into the complex molecular determinants of allergic disease. Individuals with similar clinical diagnoses do not necessarily have similar disease etiologies, natural histories, or responses to treatment. This heterogeneity contributes to the ineffective response to treatment leading to an annual estimated cost of $350 billion in the USA alone. There has been a recent focus to deconvolute the clinical heterogeneity of allergic diseases into specific endotypes using molecular and omics approaches. Endotypes are a means to classify patients based on the underlying pathophysiological mechanisms involving distinct functions or treatment response. The advent of high-throughput molecular omics, immunophenotyping, and bioinformatics methods including machine learning algorithms is facilitating the development of endotype-based diagnosis. As we move to the next decade, we should truly start treating clinical endotypes not clinical phenotype. This review highlights current efforts taking place to improve allergic disease endotyping via molecular omics profiling, immunophenotyping, and machine learning approaches in the context of precision diagnostics in allergic diseases. Graphical Abstract.
Collapse
|
5
|
Croteau-Chonka DC, Raby BA. TREM-1 Response Signatures Common to Expression Profiles of Both Asthma Affection and Asthma Control. Am J Respir Crit Care Med 2019; 198:401-404. [PMID: 29570347 DOI: 10.1164/rccm.201709-1964le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Benjamin A Raby
- 1 Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts
| |
Collapse
|
6
|
Affiliation(s)
- Lawrence E K Gray
- 1 School of Medicine, Deakin University, Geelong, Victoria, Australia; and
| | - Peter D Sly
- 2 Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
7
|
Bennett TD, Callahan TJ, Feinstein JA, Ghosh D, Lakhani SA, Spaeder MC, Szefler SJ, Kahn MG. Data Science for Child Health. J Pediatr 2019; 208:12-22. [PMID: 30686480 PMCID: PMC6486872 DOI: 10.1016/j.jpeds.2018.12.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/11/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Tellen D Bennett
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO; CU Data Science to Patient Value (D2V), University of Colorado School of Medicine, Aurora, CO; Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO; Adult and Child Consortium for Outcomes Research and Delivery Science (ACCORDS), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO; Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO.
| | - Tiffany J Callahan
- Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - James A Feinstein
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO; Adult and Child Consortium for Outcomes Research and Delivery Science (ACCORDS), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Debashis Ghosh
- CU Data Science to Patient Value (D2V), University of Colorado School of Medicine, Aurora, CO; Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO; Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Michael C Spaeder
- Pediatric Critical Care, University of Virginia School of Medicine, Charlottesville, VA
| | - Stanley J Szefler
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO; Adult and Child Consortium for Outcomes Research and Delivery Science (ACCORDS), University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Michael G Kahn
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO; Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
8
|
Abstract
The recent Lancet commission has highlighted that "asthma" should be used to describe a clinical syndrome of wheeze, breathlessness, chest tightness, and sometimes cough. The next step is to deconstruct the airway into components of fixed and variable airflow obstruction, inflammation, infection and altered cough reflex, setting the airway disease in the context of extra-pulmonary co-morbidities and social and environmental factors. The emphasis is always on delineating treatable traits, including variable airflow obstruction caused by airway smooth muscle constriction (treated with short- and long-acting β-2 agonists), eosinophilic airway inflammation (treated with inhaled corticosteroids) and chronic bacterial infection (treated with antibiotics with benefit if it is driving the disease). It is also important not to over-treat the untreatable, such as fixed airflow obstruction. These can all be determined using simple, non-invasive tests such as spirometry before and after acute administration of a bronchodilator (reversible airflow obstruction); peripheral blood eosinophil count, induced sputum, exhaled nitric oxide (airway eosinophilia); and sputum or cough swab culture (bacterial infection). Additionally, the pathophysiology of risk domains must be considered: these are risk of an asthma attack, risk of poor airway growth, and in pre-school children, risk of progression to eosinophilic school age asthma. Phenotyping the airway will allow more precise diagnosis and targeted treatment, but it is important to move to endotypes, especially in the era of increasing numbers of biologicals. Advances in -omics technology allow delineation of pathways, which will be particularly important in TH2 low eosinophilic asthma, and also pauci-inflammatory disease. It is very important to appreciate the difficulties of cluster analysis; a patient may have eosinophilic airway disease because of a steroid resistant endotype, because of non-adherence to basic treatment, and a surge in environmental allergen burden. Sophisticated -omics approaches will be reviewed in this manuscript, but currently they are not being used in clinical practice. However, even while they are being evaluated, management of the asthmas can and should be improved by considering the pathophysiologies of the different airway diseases lumped under that umbrella term, using simple, non-invasive tests which are readily available, and treating accordingly.
Collapse
Affiliation(s)
- Andrew Bush
- Departments of Paediatrics and Paediatric Respiratory Medicine, Royal Brompton Harefield NHS Foundation Trust and Imperial College, London, United Kingdom
| |
Collapse
|
9
|
Translating Asthma: Dissecting the Role of Metabolomics, Genomics and Personalized Medicine. Indian J Pediatr 2018; 85:643-650. [PMID: 29185231 DOI: 10.1007/s12098-017-2520-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/27/2017] [Indexed: 01/26/2023]
Abstract
The management of asthma has largely stagnated over the last 25 years, but we are at the dawning of a new age wherein -omics technology can help us manage the disease objectively and rationally. Even in this new scientific age, getting the basics of asthma management right remains essential. The new technologies which can be applied to multiple biological samples include genomics (study of the genome), transcriptomics (gene transcription), lipidomics, proteomics and metabolomics (lipids, proteins and metabolites, respectively) and breathomics, using exhaled breath as a source of biomarkers, which is of particular interest in view of its non-invasive nature in pediatrics. Important applications will include the diagnosis of airways disease, including its components; the pathways driving airway pathology; monitoring the response to treatment; and measuring future risk (asthma attacks, poor lung growth trajectory). With the advent of a wide range of novel biologicals to treat asthma, -omics technology to personalize therapy will be especially important. The U-BIOPRED (Europe) and SARP (USA) groups have been most active in this field, especially using bronchoscopically obtained samples to perform cluster analyses to define new asthma endotypes. However, stability over time and consistency between investigators is imperfect. This is perhaps unsurprising; results of biomarker studies in asthma will be a composite of the underlying disease, the (variable) effects of adverse drivers such as allergen exposure and pollution, the effects of treatment, and the effects of adherence or otherwise to treatment. Ultimately, the aim should be an exhaled breath based tool with a rapid result that can be used as a routine in the clinic. However, at the moment, there are as yet no clinical applications in children of -omics technology.
Collapse
|