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Roe T, Silveira S, Luo Z, Osborne EL, Senthil Murugan G, Grocott MPW, Postle AD, Dushianthan A. Particles in Exhaled Air (PExA): Clinical Uses and Future Implications. Diagnostics (Basel) 2024; 14:972. [PMID: 38786270 PMCID: PMC11119244 DOI: 10.3390/diagnostics14100972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Access to distal airway samples to assess respiratory diseases is not straightforward and requires invasive procedures such as bronchoscopy and bronchoalveolar lavage. The particles in exhaled air (PExA) device provides a non-invasive means of assessing small airways; it captures distal airway particles (PEx) sized around 0.5-7 μm and contains particles of respiratory tract lining fluid (RTLF) that originate during airway closure and opening. The PExA device can count particles and measure particle mass according to their size. The PEx particles can be analysed for metabolites on various analytical platforms to quantitatively measure targeted and untargeted lung specific markers of inflammation. As such, the measurement of distal airway components may help to evaluate acute and chronic inflammatory conditions such as asthma, chronic obstructive pulmonary disease, acute respiratory distress syndrome, and more recently, acute viral infections such as COVID-19. PExA may provide an alternative to traditional methods of airway sampling, such as induced sputum, tracheal aspirate, or bronchoalveolar lavage. The measurement of specific biomarkers of airway inflammation obtained directly from the RTLF by PExA enables a more accurate and comprehensive understanding of pathophysiological changes at the molecular level in patients with acute and chronic lung diseases.
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Affiliation(s)
- Thomas Roe
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Siona Silveira
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Zixing Luo
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Optoelectronics Research Centre, University of Southampton, Southampton SO17 1BJ, UK
| | - Eleanor L Osborne
- Optoelectronics Research Centre, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Michael P W Grocott
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Anthony D Postle
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Ahilanandan Dushianthan
- General Intensive Care Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Perioperative and Critical Care Theme, NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
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2
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Antonisamy B, Shailesh H, Hani Y, Ahmed LHM, Noor S, Ahmed SY, Alfaki M, Muhayimana A, Jacob SS, Balayya SK, Soloviov O, Liu L, Mathew LS, Wang K, Tomei S, Al Massih A, Mathew R, Karim MY, Ramanjaneya M, Worgall S, Janahi IA. Sphingolipids in Childhood Asthma and Obesity (SOAP Study): A Protocol of a Cross-Sectional Study. Metabolites 2023; 13:1146. [PMID: 37999242 PMCID: PMC10673587 DOI: 10.3390/metabo13111146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
Asthma and obesity are two of the most common chronic conditions in children and adolescents. There is increasing evidence that sphingolipid metabolism is altered in childhood asthma and is linked to airway hyperreactivity. Dysregulated sphingolipid metabolism is also reported in obesity. However, the functional link between sphingolipid metabolism, asthma, and obesity is not completely understood. This paper describes the protocol of an ongoing study on sphingolipids that aims to examine the pathophysiology of sphingolipids in childhood asthma and obesity. In addition, this study aims to explore the novel biomarkers through a comprehensive multi-omics approach including genomics, genome-wide DNA methylation, RNA-Seq, microRNA (miRNA) profiling, lipidomics, metabolomics, and cytokine profiling. This is a cross-sectional study aiming to recruit 440 children from different groups: children with asthma and normal weight (n = 100), asthma with overweight or obesity (n = 100), overweight or obesity (n = 100), normal weight (n = 70), and siblings of asthmatic children with normal weight, overweight, or obesity (n = 70). These participants will be recruited from the pediatric pulmonology, pediatric endocrinology, and general pediatric outpatient clinics at Sidra Medicine, Doha, Qatar. Information will be obtained from self-reported questionnaires on asthma, quality of life, food frequency (FFQ), and a 3-day food diary that are completed by the children and their parents. Clinical measurements will include anthropometry, blood pressure, biochemistry, bioelectrical impedance, and pulmonary function tests. Blood samples will be obtained for sphingolipid analysis, serine palmitoyltransferase (SPT) assay, whole-genome sequencing (WGS), genome-wide DNA methylation study, RNA-Seq, miRNA profiling, metabolomics, lipidomics, and cytokine analysis. Group comparisons of continuous outcome variables will be carried out by a one-way analysis of variance or the Kruskal-Wallis test using an appropriate pairwise multiple comparison test. The chi-squared test or a Fisher's exact test will be used to test the associations between categorical variables. Finally, multivariate analysis will be carried out to integrate the clinical data with multi-omics data. This study will help us to understand the role of dysregulated sphingolipid metabolism in obesity and asthma. In addition, the multi-omics data from the study will help to identify novel genetic and epigenetic signatures, inflammatory markers, and mechanistic pathways that link asthma and obesity in children. Furthermore, the integration of clinical and multi-omics data will help us to uncover the potential interactions between these diseases and to offer a new paradigm for the treatment of pediatric obesity-associated asthma.
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Affiliation(s)
- Belavendra Antonisamy
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
| | - Harshita Shailesh
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
| | - Yahya Hani
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
| | - Lina Hayati M. Ahmed
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
| | - Safa Noor
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
| | - Salma Yahya Ahmed
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
| | - Mohamed Alfaki
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
| | - Abidan Muhayimana
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
| | - Shana Sunny Jacob
- Analytical Chemistry Core, Advanced Diagnostic Core Facilities, Sidra Medicine, Doha P.O. Box 26999, Qatar; (S.S.J.); (S.K.B.)
| | - Saroja Kotegar Balayya
- Analytical Chemistry Core, Advanced Diagnostic Core Facilities, Sidra Medicine, Doha P.O. Box 26999, Qatar; (S.S.J.); (S.K.B.)
| | - Oleksandr Soloviov
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha P.O. Box 26999, Qatar; (O.S.); (L.L.); (L.S.M.); (K.W.)
| | - Li Liu
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha P.O. Box 26999, Qatar; (O.S.); (L.L.); (L.S.M.); (K.W.)
| | - Lisa Sara Mathew
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha P.O. Box 26999, Qatar; (O.S.); (L.L.); (L.S.M.); (K.W.)
| | - Kun Wang
- Clinical Genomics Laboratory, Integrated Genomics Services, Sidra Medicine, Doha P.O. Box 26999, Qatar; (O.S.); (L.L.); (L.S.M.); (K.W.)
| | - Sara Tomei
- Omics Core, Integrated Genomics Services, Sidra Medicine, Doha P.O. Box 26999, Qatar; (S.T.); (A.A.M.); (R.M.)
| | - Alia Al Massih
- Omics Core, Integrated Genomics Services, Sidra Medicine, Doha P.O. Box 26999, Qatar; (S.T.); (A.A.M.); (R.M.)
| | - Rebecca Mathew
- Omics Core, Integrated Genomics Services, Sidra Medicine, Doha P.O. Box 26999, Qatar; (S.T.); (A.A.M.); (R.M.)
| | - Mohammed Yousuf Karim
- Department of Pathology, Sidra Medicine, Doha P.O. Box 26999, Qatar;
- College of Medicine, Qatar University, Doha P.O. Box 2713, Qatar
| | - Manjunath Ramanjaneya
- Qatar Metabolic Institute, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar;
- Translational Research Institute, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Stefan Worgall
- Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Ibrahim A. Janahi
- Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar; (B.A.); (H.S.); (Y.H.); (L.H.M.A.); (S.N.); (S.Y.A.); (M.A.); (A.M.)
- Department of Pediatrics, Weill Cornell Medicine-Qatar, Doha P.O. Box 24144, Qatar
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Nakamura K, Fujita Y, Chen H, Somekawa K, Kashizaki F, Koizumi H, Takahashi K, Horita N, Hara Y, Muro S, Kaneko T. The Effectiveness and Safety of Long-Term Macrolide Therapy for COPD in Stable Status: A Systematic Review and Meta-Analysis. Diseases 2023; 11:152. [PMID: 37987263 PMCID: PMC10660475 DOI: 10.3390/diseases11040152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
Background: Chronic obstructive pulmonary disease (COPD) is a prevalent condition with fewer treatments available as the severity increases. Previous systematic reviews have demonstrated the benefits of long-term macrolide use. However, the therapeutic differences between different macrolides and the optimal duration of use remain unclear. Methods: A systematic review and meta-analysis were conducted to assess the effectiveness of long-term macrolide use in reducing COPD exacerbations, compare the therapeutic differences among macrolides, and determine the appropriate treatment duration. Four databases (PubMed, Cochrane Library, Web of Science, and ICHU-SHI) were searched until 20 March 2023, and a random-effects model was used to calculate the pooled effect. Results: The meta-analysis included nine randomized controlled trials involving 1965 patients. The analysis revealed an odds ratio (OR) of 0.34 (95% confidence interval [CI] 0.19, 0.59, p < 0.001) for the reduction in exacerbation frequency. Notably, only azithromycin or erythromycin showed suppression of COPD exacerbations. The ORs for reducing exacerbation frequency per year and preventing hospitalizations were -0.50 (95% CI: -0.81, -0.19; p = 0.001) and 0.60 (95% CI: 0.3, 0.97; p = 0.04), respectively. Statistical analyses showed no significant differences between three- and six-month macrolide prescriptions. However, studies involving a twelve-month prescription showed an OR of 0.27 (95% CI: 0.11, 0.68; p = 0.005; I2 = 81%). Although a significant improvement in St George's Respiratory Questionnaire (SGRQ) total scores was observed with a mean difference of -4.42 (95% CI: -9.0, 0.16; p = 0.06; I2 = 94%), the minimal clinically important difference was not reached. While no adverse effects were observed between the two groups, several studies have reported an increase in bacterial resistance. Conclusions: Long-term use of azithromycin or erythromycin suppresses COPD exacerbations, and previous studies have supported the advantages of a 12-month macrolide prescription over a placebo.
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Affiliation(s)
- Kazunori Nakamura
- Department of Respiratory Medicine, Saiseikai Kumamoto Hospital, Kumamoto 861-4193, Japan;
| | - Yukio Fujita
- Department of Respiratory Medicine, Nara Medical University, Nara 634-8522, Japan; (Y.F.); (S.M.)
| | - Hao Chen
- Department of Pulmonology, Yokohama City University Hospital, Yokohama 236-0004, Japan; (K.S.); (Y.H.); (T.K.)
- Department of Respiratory Medicine, Yokohama Minami Kyousai Hospital, Yokohama 236-0037, Japan; (F.K.); (H.K.); (K.T.)
| | - Kohei Somekawa
- Department of Pulmonology, Yokohama City University Hospital, Yokohama 236-0004, Japan; (K.S.); (Y.H.); (T.K.)
| | - Fumihiro Kashizaki
- Department of Respiratory Medicine, Yokohama Minami Kyousai Hospital, Yokohama 236-0037, Japan; (F.K.); (H.K.); (K.T.)
| | - Harumi Koizumi
- Department of Respiratory Medicine, Yokohama Minami Kyousai Hospital, Yokohama 236-0037, Japan; (F.K.); (H.K.); (K.T.)
| | - Kenichi Takahashi
- Department of Respiratory Medicine, Yokohama Minami Kyousai Hospital, Yokohama 236-0037, Japan; (F.K.); (H.K.); (K.T.)
| | - Nobuyuki Horita
- Chemotherapy Center, Yokohama City University Hospital, Yokohama 236-0004, Japan;
| | - Yu Hara
- Department of Pulmonology, Yokohama City University Hospital, Yokohama 236-0004, Japan; (K.S.); (Y.H.); (T.K.)
| | - Shigeo Muro
- Department of Respiratory Medicine, Nara Medical University, Nara 634-8522, Japan; (Y.F.); (S.M.)
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Hospital, Yokohama 236-0004, Japan; (K.S.); (Y.H.); (T.K.)
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4
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Guryanova SV. Immunomodulation, Bioavailability and Safety of Bacteriocins. Life (Basel) 2023; 13:1521. [PMID: 37511896 PMCID: PMC10381439 DOI: 10.3390/life13071521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
The rise of antibiotic-resistant bacteria and the emergence of new pathogens have created a need for new strategies to fight against infectious diseases. One promising approach is the use of antimicrobial peptides produced by a certain species of bacteria, known as bacteriocins, which are active against other strains of the same or related species. Bacteriocins can help in the treatment and prevention of infectious diseases. Moreover, bacteriocins can be obtained in prokaryotic organisms, and contribute s to their widespread use. While the use of bacteriocins is currently limited to the food industry (for example, nisin is used as a preservative, E234), a large number of studies on their microbicidal properties suggest that their use in medicine may increase in the foreseeable future. However, for the successful use of bacteriocins in medicine, it is necessary to understand their effect on the immune system, especially in cases where immunity is weakened due to infectious processes, oncological, allergic, or autoimmune diseases. Studies on the immuno-modulatory activity of bacteriocins in animal models and human cells have revealed their ability to induce both pro-inflammatory and anti-inflammatory factors involved in the implementation of innate immunity. The influence of bacteriocins on acquired immunity is revealed by an increase in the number of T-lymphocytes with a simultaneous decrease in B-lymphocyte levels, which makes them attractive substances for reducing inflammation. The widespread use of bacteriocins in the food industry, their low toxicity, and their broad and narrow specificity are reasons for researchers to pay attention to their immunomodulatory properties and explore their medical applications. Inflammation regulation by bacteriocins can be used in the treatment of various pathologies. The aim of the review was to analyze scientific publications on the immunomodulatory activity, bioavailability, and safety of bacteriocins in order to use the data obtained to organize preclinical and clinical studies.
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Affiliation(s)
- Svetlana V Guryanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Medical Institute, Peoples' Friendship University of Russia (RUDN University) of the Ministry of Science and Higher Education of the Russian Federation, 117198 Moscow, Russia
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Sputum-Rheology-Based Strategy for Guiding Azithromycin Prescription in COPD Patients with Frequent Exacerbations: A Randomized, Controlled Study (“COPD CARhE”). Biomedicines 2023; 11:biomedicines11030740. [PMID: 36979719 PMCID: PMC10045420 DOI: 10.3390/biomedicines11030740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
(1) Background: We have previously shown that sputum rheology can discriminate between patients with COPD and other muco-obstructive lung diseases, and that it is correlated with mucin content and sputum eosinophilia. We now hypothesize that it could be a more-accurate guide than clinical evaluation for the prescription of azithromycin to prevent exacerbations of COPD and to reduce exposure to antibiotics; (2) Methods: “COPD CaRhe” is a multicentric, randomized, controlled trial comparing outcomes in two parallel arms (36 vs. 36 patients). Patients will be recruited in the university hospitals of Montpellier, Bordeaux, and Toulouse, in France, and they should have a diagnosis of COPD with frequent exacerbations (≥3/year). Enrollment will occur during a routine visit to a respiratory department, and follow-up visits will occur every 3 months for a period of 1 year. At each visit, a 3-month prescription of azithromycin will be provided to those patients who obtain a score of <70 on the Cough and Sputum Assessment Questionnaire (CASA-Q) or a critical stress score of σc > 39 on a rheological assessment of sputum, depending upon their randomization group. The primary outcome will be the number of exacerbations of COPD; (3) Discussion: By using sputum rheology, the COPD CaRhe study may provide clinicians with an objective biomarker to guide the prescription of azithromycin while reducing the cumulative exposure to macrolides.
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Guryanova SV, Kataeva A. Inflammation Regulation by Bacterial Molecular Patterns. Biomedicines 2023; 11:biomedicines11010183. [PMID: 36672691 PMCID: PMC9855958 DOI: 10.3390/biomedicines11010183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Stimulation of innate immunity by bacterial molecular patterns can induce an enhanced cellular immune response to pathogens that are associated with innate immune memory shaped by epigenetic changes. Immunological memory can be expressed in the acceleration/intensification of inflammation, as well as in the exact opposite-to maintain tolerance and non-response to a repeated stimulus. Tolerance is one of the central concepts of immunity and is ensured by the consistency of all parts of the immune response. The severe consequences of inflammation force researchers to study in detail all stages of the downstream pathways that are activated after exposure to a stimulus, while the formation of non-response to a pro-inflammatory stimulus has not yet received a detailed description. Elucidation of the mechanism of tolerance is an urgent task for the prevention and treatment of inflammatory diseases. The aim of this investigation was to study the dynamic changes in the gene expression of A20 and ATF3, the inflammation suppressors, against the background of the expression of the genes of the innate immunity receptors TLR4 and NOD2 and the pro-inflammatory cytokine TNF-α under the influence of TLR4 and NOD2 agonists, lipopolysaccharide (LPS) and glucosaminylmuramyl dipeptide (GMDP). The mechanism of inflammation regulation by bioregulators of bacterial origin-LPS and GMDP-was evaluated in vitro in human peripheral blood mononuclear cells and in vivo after i.p. administration of LPS and GMDP to mice. Gene expression was assessed by RT-PCR. Innate immune receptors and the pro-inflammatory cytokine TNF-α were found to develop early in response to LPS and GMDP, both in vitro and in vivo. Genes of cytosolic proteins controlling inflammation (A20 and ATF3) were expressed later. Prior exposure of the innate immune system to LPS and muramyl peptides may modulate host defense against acute inflammation. As a result of the study, new data were obtained on dynamic changes in deubiquitinase A20 and the transcription factor ATF3, which are involved in the limitation and suppression of inflammatory reactions caused by fragments of bacterial cell walls-LPS and GMDP. Thus, bioregulators of bacterial origin LPS and GMDP, along with pro-inflammatory factors, activate the expression of genes that suppress inflammation, which should be considered when analyzing data from studies of the pro-inflammatory properties of LPS and GMDP and when developing drugs based on them.
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Affiliation(s)
- Svetlana V. Guryanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Ministry of Science and Higher Education of the Russian Federation, 117997 Moscow, Russia
- Medical Institute, Peoples’ Friendship University of Russia (RUDN University) of the Ministry of Science and Higher Education of the Russian Federation, 117198 Moscow, Russia
- Correspondence: ; Tel.: +7-9153150073
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7
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Innate Immunity Mechanisms in Marine Multicellular Organisms. Mar Drugs 2022; 20:md20090549. [PMID: 36135738 PMCID: PMC9505182 DOI: 10.3390/md20090549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/27/2022] Open
Abstract
The innate immune system provides an adequate response to stress factors and pathogens through pattern recognition receptors (PRRs), located on the surface of cell membranes and in the cytoplasm. Generally, the structures of PRRs are formed by several domains that are evolutionarily conserved, with a fairly high degree of homology in representatives of different species. The orthologs of TLRs, NLRs, RLRs and CLRs are widely represented, not only in marine chordates, but also in invertebrates. Study of the interactions of the most ancient marine multicellular organisms with microorganisms gives us an idea of the evolution of molecular mechanisms of protection against pathogens and reveals new functions of already known proteins in ensuring the body’s homeostasis. The review discusses innate immunity mechanisms of protection of marine invertebrate organisms against infections, using the examples of ancient multicellular hydroids, tunicates, echinoderms, and marine worms in the context of searching for analogies with vertebrate innate immunity. Due to the fact that mucous membranes first arose in marine invertebrates that have existed for several hundred million years, study of their innate immune system is both of fundamental importance in terms of understanding molecular mechanisms of host defense, and of practical application, including the search of new antimicrobial agents for subsequent use in medicine, veterinary and biotechnology.
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8
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Guryanova SV. Regulation of Immune Homeostasis via Muramyl Peptides-Low Molecular Weight Bioregulators of Bacterial Origin. Microorganisms 2022; 10:microorganisms10081526. [PMID: 36013944 PMCID: PMC9413341 DOI: 10.3390/microorganisms10081526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Metabolites and fragments of bacterial cells play an important role in the formation of immune homeostasis. Formed in the course of evolution, symbiotic relationships between microorganisms and a macroorganism are manifested, in particular, in the regulation of numerous physiological functions of the human body by the innate immunity receptors. Low molecular weight bioregulators of bacterial origin have recently attracted more and more attention as drugs in the prevention and composition of complex therapy for a wide range of diseases of bacterial and viral etiology. Signaling networks show cascades of causal relationships of deterministic phenomena that support the homeostasis of multicellular organisms at different levels. To create networks, data from numerous biomedical and clinical research databases were used to prepare expert systems for use in pharmacological and biomedical research with an emphasis on muramyl dipeptides. Muramyl peptides are the fragments of the cell wall of Gram-positive and Gram-negative bacteria. Binding of muramyl peptides with intracellular NOD2 receptors is crucial for an immune response on pathogens. Depending on the microenvironment and duration of action, muramyl peptides possess positive or negative regulation of inflammation. Other factors, such as genetic, pollutions, method of application and stress also contribute and should be taken into account. A system biology approach should be used in order to systemize all experimental data for rigorous analysis, with the aim of understanding intrinsic pathways of homeostasis, in order to define precise medicine therapy and drug design.
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Affiliation(s)
- Svetlana V Guryanova
- Medical Institute, Peoples' Friendship University of Russia (RUDN University) of the Ministry of Science and Higher Education of the Russian Federation, 117198 Moscow, Russia
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9
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Arellano-Orden E, Calero Acuña C, Sánchez-López V, López Ramírez C, Otero-Candelera R, Marín-Hinojosa C, López Campos J. Cellular mechanisms involved in the pathogenesis of airway remodeling in chronic lung disease. Eur Clin Respir J 2022; 9:2097377. [PMID: 35832729 PMCID: PMC9272929 DOI: 10.1080/20018525.2022.2097377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- E. Arellano-Orden
- Unidad Médico Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/Universidad de SevillaUnidad Médico Quirúrgica de Enfermedades Respiratorias,Quirúrgica, Seville, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - C. Calero Acuña
- Unidad Médico Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/Universidad de SevillaUnidad Médico Quirúrgica de Enfermedades Respiratorias,Quirúrgica, Seville, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - V. Sánchez-López
- Unidad Médico Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/Universidad de SevillaUnidad Médico Quirúrgica de Enfermedades Respiratorias,Quirúrgica, Seville, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - C. López Ramírez
- Unidad Médico Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/Universidad de SevillaUnidad Médico Quirúrgica de Enfermedades Respiratorias,Quirúrgica, Seville, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - R. Otero-Candelera
- Unidad Médico Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/Universidad de SevillaUnidad Médico Quirúrgica de Enfermedades Respiratorias,Quirúrgica, Seville, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - C. Marín-Hinojosa
- Unidad Médico Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/Universidad de SevillaUnidad Médico Quirúrgica de Enfermedades Respiratorias,Quirúrgica, Seville, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jl López Campos
- Unidad Médico Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/Universidad de SevillaUnidad Médico Quirúrgica de Enfermedades Respiratorias,Quirúrgica, Seville, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
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10
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Immunomodulatory and Allergenic Properties of Antimicrobial Peptides. Int J Mol Sci 2022; 23:ijms23052499. [PMID: 35269641 PMCID: PMC8910669 DOI: 10.3390/ijms23052499] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023] Open
Abstract
With the growing problem of the emergence of antibiotic-resistant bacteria, the search for alternative ways to combat bacterial infections is extremely urgent. While analyzing the effect of antimicrobial peptides (AMPs) on immunocompetent cells, their effect on all parts of the immune system, and on humoral and cellular immunity, is revealed. AMPs have direct effects on neutrophils, monocytes, dendritic cells, T-lymphocytes, and mast cells, participating in innate immunity. They act on B-lymphocytes indirectly, enhancing the induction of antigen-specific immunity, which ultimately leads to the activation of adaptive immunity. The adjuvant activity of AMPs in relation to bacterial and viral antigens was the reason for their inclusion in vaccines and made it possible to formulate the concept of a “defensin vaccine” as an innovative basis for constructing vaccines. The immunomodulatory function of AMPs involves their influence on cells in the nearest microenvironment, recruitment and activation of other cells, supporting the response to pathogenic microorganisms and completing the inflammatory process, thus exhibiting a systemic effect. For the successful use of AMPs in medical practice, it is necessary to study their immunomodulatory activity in detail, taking into account their pleiotropy. The degree of maturity of the immune system and microenvironment can contribute to the prevention of complications and increase the effectiveness of therapy, since AMPs can suppress inflammation in some circumstances, but aggravate the response and damage of organism in others. It should also be taken into account that the real functions of one or another AMP depend on the types of total regulatory effects on the target cell, and not only on properties of an individual peptide. A wide spectrum of biological activity, including direct effects on pathogens, inactivation of bacterial toxins and influence on immunocompetent cells, has attracted the attention of researchers, however, the cytostatic activity of AMPs against normal cells, as well as their allergenic properties and low stability to host proteases, are serious limitations for the medical use of AMPs. In this connection, the tasks of searching for compounds that selectively affect the target and development of an appropriate method of application become critically important. The scope of this review is to summarize the current concepts and newest advances in research of the immunomodulatory activity of natural and synthetic AMPs, and to examine the prospects and limitations of their medical use.
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11
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Guryanova SV, Gigani OB, Gudima GO, Kataeva AM, Kolesnikova NV. Dual Effect of Low-Molecular-Weight Bioregulators of Bacterial Origin in Experimental Model of Asthma. Life (Basel) 2022; 12:life12020192. [PMID: 35207480 PMCID: PMC8879587 DOI: 10.3390/life12020192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Asthma is one of the most common noncommunicable diseases, affecting over 200 million people. A large number of drugs control asthma attacks, but there is no effective therapy. Identification of reasons for asthma and preventing this disease is a relevant task. The influence of bacterial components is necessary for the normal development of the immune system and the formation of an adequate immune response to antigens. In the absence of microorganisms or their insufficient exposure, the prerequisites are formed for excessive reactivity to harmless antigens. In the present study, we analyzed cellular and humoral factors in a standard mouse model of OVA-induced asthma modified by 5-fold intraperitoneal injection of bacterial cell wall fragments of glucosaminylmuramyl dipeptide (GMDP) 5 μg/animal or 1 μg lipopolysaccharide (LPS) per animal for 5 days before sensitization by ovalbumin (OVA). Preliminary administration of LPS or GMDP to animals significantly reduced goblet cells as well as the number of neutrophils, lymphocytes, and eosinophils in bronchoalveolar lavage, wherein GMDP corrected neutrophilia to a 2-fold degree, and LPS reduced the severity of eosinophilia by 1.9 times. With OVA administration of GMDP or LPS at the sensitization stage, an increase in the total number of bronchoalveolar lavage cells due to neutrophils, macrophages, lymphocytes, and eosinophils in relation to the group with asthma without GMDP or LPS was observed. The administration of GMDP or LPS to normal mice without asthma for 5 days had no statistically significant effect on the change in the number and population composition of cells in bronchoalveolar lavage in comparison with the control group receiving PBS. As a result of a study in a mouse model of asthma, a dual effect of LPS and GMDP was established: the introduction of LPS or GMDP before sensitization reduces neutrophilia and eosinophilia, while the introduction of LPS or GMDP together with an allergen significantly increases neutrophilia and eosinophilia. The study of the immunoglobulin status shows that in normal-asthma mice, GMDP and LPS slightly increase IgA in bronchoalveolar lavage; at the same time, in the asthma model, injections of GMDP or LPS before sensitization contribute to a significant decrease in IgA (2.6 times and 2.1 times, respectively) in BALF and IgE (2.2 times and 2.0 times, respectively) in blood serum. In an experimental model of asthma, the effect of GMDP and LPS was multidirectional: when they are repeatedly administered before sensitization, the bacterial components significantly reduce the severity of the allergic process, while in the case of a joint injection with an allergen, they increase the influx of macrophages, lymphocytes, and neutrophils into the lungs, which can aggravate the course of pathological process. Thus, the insufficient effect of antigens of a bacterial nature, in particular, with prolonged use of antibiotics can be compensated for by substances based on low-molecular-weight bioregulators of bacterial origin to establish the missing signals for innate immunity receptors, whose constant activation at a certain level is necessary to maintain homeostasis.
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Affiliation(s)
- Svetlana V. Guryanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Ministry of Science and Higher Education of the Russian Federation, 117997 Moscow, Russia
- Medical Institute, Peoples’ Friendship University of Russia (RUDN University), Ministry of Science and Higher Education of the Russian Federation, 117198 Moscow, Russia; (O.B.G.); (A.M.K.)
- Correspondence:
| | - Olga B. Gigani
- Medical Institute, Peoples’ Friendship University of Russia (RUDN University), Ministry of Science and Higher Education of the Russian Federation, 117198 Moscow, Russia; (O.B.G.); (A.M.K.)
| | - Georgii O. Gudima
- National Research Center-Institute of Immunology of the Federal Medico-Biological Agency, 115522 Moscow, Russia;
| | - Anastasiya M. Kataeva
- Medical Institute, Peoples’ Friendship University of Russia (RUDN University), Ministry of Science and Higher Education of the Russian Federation, 117198 Moscow, Russia; (O.B.G.); (A.M.K.)
| | - Natalya V. Kolesnikova
- Department of Clinical Immunology, Kuban State Medical University, Ministry of Health of the Russian Federation, 350063 Krasnodar, Russia;
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12
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Créquit P, Mansouri G, Benchoufi M, Vivot A, Ravaud P. Mapping of Crowdsourcing in Health: Systematic Review. J Med Internet Res 2018; 20:e187. [PMID: 29764795 PMCID: PMC5974463 DOI: 10.2196/jmir.9330] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/10/2018] [Accepted: 03/14/2018] [Indexed: 11/22/2022] Open
Abstract
Background Crowdsourcing involves obtaining ideas, needed services, or content by soliciting Web-based contributions from a crowd. The 4 types of crowdsourced tasks (problem solving, data processing, surveillance or monitoring, and surveying) can be applied in the 3 categories of health (promotion, research, and care). Objective This study aimed to map the different applications of crowdsourcing in health to assess the fields of health that are using crowdsourcing and the crowdsourced tasks used. We also describe the logistics of crowdsourcing and the characteristics of crowd workers. Methods MEDLINE, EMBASE, and ClinicalTrials.gov were searched for available reports from inception to March 30, 2016, with no restriction on language or publication status. Results We identified 202 relevant studies that used crowdsourcing, including 9 randomized controlled trials, of which only one had posted results at ClinicalTrials.gov. Crowdsourcing was used in health promotion (91/202, 45.0%), research (73/202, 36.1%), and care (38/202, 18.8%). The 4 most frequent areas of application were public health (67/202, 33.2%), psychiatry (32/202, 15.8%), surgery (22/202, 10.9%), and oncology (14/202, 6.9%). Half of the reports (99/202, 49.0%) referred to data processing, 34.6% (70/202) referred to surveying, 10.4% (21/202) referred to surveillance or monitoring, and 5.9% (12/202) referred to problem-solving. Labor market platforms (eg, Amazon Mechanical Turk) were used in most studies (190/202, 94%). The crowd workers’ characteristics were poorly reported, and crowdsourcing logistics were missing from two-thirds of the reports. When reported, the median size of the crowd was 424 (first and third quartiles: 167-802); crowd workers’ median age was 34 years (32-36). Crowd workers were mainly recruited nationally, particularly in the United States. For many studies (58.9%, 119/202), previous experience in crowdsourcing was required, and passing a qualification test or training was seldom needed (11.9% of studies; 24/202). For half of the studies, monetary incentives were mentioned, with mainly less than US $1 to perform the task. The time needed to perform the task was mostly less than 10 min (58.9% of studies; 119/202). Data quality validation was used in 54/202 studies (26.7%), mainly by attention check questions or by replicating the task with several crowd workers. Conclusions The use of crowdsourcing, which allows access to a large pool of participants as well as saving time in data collection, lowering costs, and speeding up innovations, is increasing in health promotion, research, and care. However, the description of crowdsourcing logistics and crowd workers’ characteristics is frequently missing in study reports and needs to be precisely reported to better interpret the study findings and replicate them.
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Affiliation(s)
- Perrine Créquit
- INSERM UMR1153, Methods Team, Epidemiology and Statistics Sorbonne Paris Cité Research Center, Paris Descartes University, Paris, France.,Centre d'Epidémiologie Clinique, Hôpital Hôtel Dieu, Assistance Publique des Hôpitaux de Paris, Paris, France.,Cochrane France, Paris, France
| | - Ghizlène Mansouri
- INSERM UMR1153, Methods Team, Epidemiology and Statistics Sorbonne Paris Cité Research Center, Paris Descartes University, Paris, France
| | - Mehdi Benchoufi
- Centre d'Epidémiologie Clinique, Hôpital Hôtel Dieu, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Alexandre Vivot
- INSERM UMR1153, Methods Team, Epidemiology and Statistics Sorbonne Paris Cité Research Center, Paris Descartes University, Paris, France.,Centre d'Epidémiologie Clinique, Hôpital Hôtel Dieu, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Philippe Ravaud
- INSERM UMR1153, Methods Team, Epidemiology and Statistics Sorbonne Paris Cité Research Center, Paris Descartes University, Paris, France.,Centre d'Epidémiologie Clinique, Hôpital Hôtel Dieu, Assistance Publique des Hôpitaux de Paris, Paris, France.,Cochrane France, Paris, France.,Department of Epidemiology, Columbia University, Mailman School of Public Health, New York, NY, United States
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13
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Iskandar AR, Titz B, Sewer A, Leroy P, Schneider T, Zanetti F, Mathis C, Elamin A, Frentzel S, Schlage WK, Martin F, Ivanov NV, Peitsch MC, Hoeng J. Systems toxicology meta-analysis of in vitro assessment studies: biological impact of a candidate modified-risk tobacco product aerosol compared with cigarette smoke on human organotypic cultures of the aerodigestive tract. Toxicol Res (Camb) 2017; 6:631-653. [PMID: 30090531 PMCID: PMC6062142 DOI: 10.1039/c7tx00047b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/26/2017] [Indexed: 12/22/2022] Open
Abstract
Systems biology combines comprehensive molecular analyses with quantitative modeling to understand the characteristics of a biological system as a whole. Leveraging a similar approach, systems toxicology aims to decipher complex biological responses following exposures. This work reports a systems toxicology meta-analysis in the context of in vitro assessment of a candidate modified-risk tobacco product (MRTP) using three human organotypic cultures of the aerodigestive tract (buccal, bronchial, and nasal epithelia). Complementing a series of functional measures, a causal network enrichment analysis of transcriptomic data was used to compare quantitatively the biological impact of aerosol from the Tobacco Heating System (THS) 2.2, a candidate MRTP, with 3R4F cigarette smoke (CS) at similar nicotine concentrations. Lower toxicity was observed in all cultures following exposure to THS2.2 aerosol compared with 3R4F CS. Because of their morphological differences, a smaller exposure impact was observed in the buccal (stratified epithelium) compared with the bronchial and nasal (pseudostratified epithelium). However, the causal network enrichment approach supported a similar mechanistic impact of CS across the three cultures, including the impact on xenobiotic, oxidative stress, and inflammatory responses. At comparable nicotine concentrations, THS2.2 aerosol elicited reduced and more transient effects on these processes. To demonstrate the benefits of additional data modalities, we employed a newly established targeted mass-spectrometry marker panel to further confirm the reduced cellular stress responses elicited by THS2.2 aerosol compared with 3R4F CS in the nasal culture. Overall, this work demonstrates the applicability and robustness of the systems toxicology approach for in vitro inhalation toxicity assessment.
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Affiliation(s)
- A R Iskandar
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - B Titz
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - A Sewer
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - P Leroy
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - T Schneider
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - F Zanetti
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - C Mathis
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - A Elamin
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - S Frentzel
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - W K Schlage
- Biology consultant , Max-Baermann-Str. 21 , 51429 Bergisch Gladbach , Germany
| | - F Martin
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - N V Ivanov
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - M C Peitsch
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - J Hoeng
- PMI R&D , Philip Morris Products S.A. (part of the Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
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14
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Talikka M, Martin F, Sewer A, Vuillaume G, Leroy P, Luettich K, Chaudhary N, Peck MJ, Peitsch MC, Hoeng J. Mechanistic Evaluation of the Impact of Smoking and Chronic Obstructive Pulmonary Disease on the Nasal Epithelium. CLINICAL MEDICINE INSIGHTS-CIRCULATORY RESPIRATORY AND PULMONARY MEDICINE 2017; 11:1179548417710928. [PMID: 28620266 PMCID: PMC5466113 DOI: 10.1177/1179548417710928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/04/2017] [Indexed: 12/27/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the major causes of chronic morbidity and mortality worldwide. The development of markers of COPD onset is hampered by the lack of accessibility to the primary target tissue, and there is a need to consider other sample sources as surrogates for biomarker research. Airborne toxicants pass through the nasal epithelium before reaching the lower airways, and the similarity with bronchial histology makes it an attractive surrogate for lower airways. In this work, we describe the transcriptomics findings from the nasal epithelia of subjects enrolled in a clinical study focusing on the identification of COPD biomarkers. Transcriptomic data were analyzed using the biological network approach that enabled us to pinpoint the biological processes affected in the upper respiratory tract in response to smoking and mild-to-moderate COPD. Our results indicated that nasal and lower airway immune responses were considerably different in COPD subjects and caution should be exercised when using upper airway samples as a surrogate for the lower airway. Nevertheless, the network approach described here could present a sensitive means of identifying smokers at risk of developing COPD.
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Affiliation(s)
- Marja Talikka
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Florian Martin
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Alain Sewer
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Grégory Vuillaume
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Patrice Leroy
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Karsta Luettich
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Nveed Chaudhary
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Michael J Peck
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris Products SA and Research & Development (R&D), Philip Morris International, Neuchâtel, Switzerland
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Hartung T, FitzGerald RE, Jennings P, Mirams GR, Peitsch MC, Rostami-Hodjegan A, Shah I, Wilks MF, Sturla SJ. Systems Toxicology: Real World Applications and Opportunities. Chem Res Toxicol 2017; 30:870-882. [PMID: 28362102 PMCID: PMC5396025 DOI: 10.1021/acs.chemrestox.7b00003] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Indexed: 01/14/2023]
Abstract
Systems Toxicology aims to change the basis of how adverse biological effects of xenobiotics are characterized from empirical end points to describing modes of action as adverse outcome pathways and perturbed networks. Toward this aim, Systems Toxicology entails the integration of in vitro and in vivo toxicity data with computational modeling. This evolving approach depends critically on data reliability and relevance, which in turn depends on the quality of experimental models and bioanalysis techniques used to generate toxicological data. Systems Toxicology involves the use of large-scale data streams ("big data"), such as those derived from omics measurements that require computational means for obtaining informative results. Thus, integrative analysis of multiple molecular measurements, particularly acquired by omics strategies, is a key approach in Systems Toxicology. In recent years, there have been significant advances centered on in vitro test systems and bioanalytical strategies, yet a frontier challenge concerns linking observed network perturbations to phenotypes, which will require understanding pathways and networks that give rise to adverse responses. This summary perspective from a 2016 Systems Toxicology meeting, an international conference held in the Alps of Switzerland, describes the limitations and opportunities of selected emerging applications in this rapidly advancing field. Systems Toxicology aims to change the basis of how adverse biological effects of xenobiotics are characterized, from empirical end points to pathways of toxicity. This requires the integration of in vitro and in vivo data with computational modeling. Test systems and bioanalytical technologies have made significant advances, but ensuring data reliability and relevance is an ongoing concern. The major challenge facing the new pathway approach is determining how to link observed network perturbations to phenotypic toxicity.
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Affiliation(s)
- Thomas Hartung
- Center
for Alternatives to Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
- University
of Konstanz, CAAT-Europe, 78457 Konstanz, Germany
| | - Rex E. FitzGerald
- Swiss
Centre for Applied Human Toxicology, University
of Basel, 4055 Basel, Switzerland
| | - Paul Jennings
- Division
of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Gary R. Mirams
- Centre
for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Manuel C. Peitsch
- Department
of Research and Development, Philip Morris
International, 2000 Neuchâtel, Switzerland
| | - Amin Rostami-Hodjegan
- Centre
for Applied Pharmacokinetic Research, University
of Manchester, Manchester M13 9PL, U.K.
- Simcyp
Limited (a Certara Company), Blades Enterprise
Centre, Sheffield S2 4SU, U.K.
| | - Imran Shah
- National
Center for Computational Toxicology, Research Triangle Park, North Carolina 27711, United States
| | - Martin F. Wilks
- Swiss
Centre for Applied Human Toxicology, University
of Basel, 4055 Basel, Switzerland
| | - Shana J. Sturla
- Department
of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland
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Arellano-Orden E, Calero-Acuña C, Cordero JA, Abad-Arranz M, Sánchez-López V, Márquez-Martín E, Ortega-Ruiz F, López-Campos JL. Specific networks of plasma acute phase reactants are associated with the severity of chronic obstructive pulmonary disease: a case-control study. Int J Med Sci 2017; 14:67-74. [PMID: 28138311 PMCID: PMC5278661 DOI: 10.7150/ijms.16907] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/01/2016] [Indexed: 12/25/2022] Open
Abstract
Objectives. A detailed understanding of the intricate relationships between different acute phase reactants (APRs) in chronic obstructive pulmonary disease (COPD) can shed new light on its clinical course. In this case-control study, we sought to identify the interaction networks of a number of plasma APRs in COPD, with a special focus on their association with disease severity. Methods. COPD cases and healthy smoking controls (3:1 ratio) were recruited in our outpatient pulmonary clinic. Cardiopulmonary exercise testing was used to rule out the presence of ischemic heart disease. All subjects were males as per protocol. Multiple plasma APRs - including α-2-macroglobulin, C-reactive protein (CRP), ferritin, fibrinogen, haptoglobin, procalcitonin (PCT), serum amyloid A (SAA), serum amyloid P, and tissue plasminogen activator (tPA) - were measured using commercial Acute Phase Bio-Plex Pro Assays and analyzed on the Bio-Plex manager software. Correlations between different APRs were investigated using a heat map. Network visualization and analyses were performed with the Cytoscape software platform. Results. A total of 96 COPD cases and 33 controls were included in the study. Plasma A2M, CRP, and SAP levels were higher in COPD patients than in controls. Circulating concentrations of haptoglobin and tPA were found to increase in parallel with the severity of the disease. Increasing disease severity was associated with distinct intricate networks of APRs, which were especially evident in advanced stages. Conclusions. We identified different networks of APRs in COPD, which were significantly associated with disease severity.
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Affiliation(s)
- Elena Arellano-Orden
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - Carmen Calero-Acuña
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain;; Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Hospital Virgen del Rocío. Seville, Spain;; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Antonio Cordero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - María Abad-Arranz
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Hospital Virgen del Rocío. Seville, Spain
| | - Verónica Sánchez-López
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - Eduardo Márquez-Martín
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain;; Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Hospital Virgen del Rocío. Seville, Spain
| | - Francisco Ortega-Ruiz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain;; Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Hospital Virgen del Rocío. Seville, Spain;; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis López-Campos
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain;; Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Hospital Virgen del Rocío. Seville, Spain;; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
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Evaluation of the Tobacco Heating System 2.2. Part 1: Description of the system and the scientific assessment program. Regul Toxicol Pharmacol 2016; 81 Suppl 2:S17-S26. [DOI: 10.1016/j.yrtph.2016.07.006] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 07/08/2016] [Indexed: 11/19/2022]
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18
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Fluck J, Madan S, Ansari S, Kodamullil AT, Karki R, Rastegar-Mojarad M, Catlett NL, Hayes W, Szostak J, Hoeng J, Peitsch M. Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw113. [PMID: 27554092 PMCID: PMC4995071 DOI: 10.1093/database/baw113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 07/07/2016] [Indexed: 01/21/2023]
Abstract
Success in extracting biological relationships is mainly dependent on the complexity of the task as well as the availability of high-quality training data. Here, we describe the new corpora in the systems biology modeling language BEL for training and testing biological relationship extraction systems that we prepared for the BioCreative V BEL track. BEL was designed to capture relationships not only between proteins or chemicals, but also complex events such as biological processes or disease states. A BEL nanopub is the smallest unit of information and represents a biological relationship with its provenance. In BEL relationships (called BEL statements), the entities are normalized to defined namespaces mainly derived from public repositories, such as sequence databases, MeSH or publicly available ontologies. In the BEL nanopubs, the BEL statements are associated with citation information and supportive evidence such as a text excerpt. To enable the training of extraction tools, we prepared BEL resources and made them available to the community. We selected a subset of these resources focusing on a reduced set of namespaces, namely, human and mouse genes, ChEBI chemicals, MeSH diseases and GO biological processes, as well as relationship types ‘increases’ and ‘decreases’. The published training corpus contains 11 000 BEL statements from over 6000 supportive text excerpts. For method evaluation, we selected and re-annotated two smaller subcorpora containing 100 text excerpts. For this re-annotation, the inter-annotator agreement was measured by the BEL track evaluation environment and resulted in a maximal F-score of 91.18% for full statement agreement. In addition, for a set of 100 BEL statements, we do not only provide the gold standard expert annotations, but also text excerpts pre-selected by two automated systems. Those text excerpts were evaluated and manually annotated as true or false supportive in the course of the BioCreative V BEL track task. Database URL:http://wiki.openbel.org/display/BIOC/Datasets
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Affiliation(s)
- Juliane Fluck
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany
| | - Sumit Madan
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany
| | - Sam Ansari
- Philip Morris International R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, Neuchâtel, 2000, Switzerland
| | - Alpha T Kodamullil
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany
| | - Reagon Karki
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany
| | | | | | - William Hayes
- Selventa, One Alewife Center, Cambridge, MA 02140, USA
| | - Justyna Szostak
- Philip Morris International R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, Neuchâtel, 2000, Switzerland
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, Neuchâtel, 2000, Switzerland
| | - Manuel Peitsch
- Philip Morris International R&D, Philip Morris Products S.A, Quai Jeanrenaud 5, Neuchâtel, 2000, Switzerland
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19
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Hirschman L, Fort K, Boué S, Kyrpides N, Islamaj Doğan R, Cohen KB. Crowdsourcing and curation: perspectives from biology and natural language processing. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw115. [PMID: 27504010 PMCID: PMC4976298 DOI: 10.1093/database/baw115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/11/2016] [Indexed: 12/27/2022]
Abstract
Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodology and its applicability to biocuration. This paper explores crowdsourcing for biocuration through several case studies that highlight different ways of leveraging 'the crowd'; these raise issues about the kind(s) of expertise needed, the motivations of participants, and questions related to feasibility, cost and quality. The paper is an outgrowth of a panel session held at BioCreative V (Seville, September 9-11, 2015). The session consisted of four short talks, followed by a discussion. In their talks, the panelists explored the role of expertise and the potential to improve crowd performance by training; the challenge of decomposing tasks to make them amenable to crowdsourcing; and the capture of biological data and metadata through community editing.Database URL: http://www.mitre.org/publications/technical-papers/crowdsourcing-and-curation-perspectives.
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Affiliation(s)
| | - Karën Fort
- University of Paris-Sorbonne/STIH Team, Paris, France
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Rezarta Islamaj Doğan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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20
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Namasivayam AA, Morales AF, Lacave ÁMF, Tallam A, Simovic B, Alfaro DG, Bobbili DR, Martin F, Androsova G, Shvydchenko I, Park J, Calvo JV, Hoeng J, Peitsch MC, Racero MGV, Biryukov M, Talikka M, Pérez MB, Rohatgi N, Díaz-Díaz N, Mandarapu R, Ruiz RA, Davidyan S, Narayanasamy S, Boué S, Guryanova S, Arbas SM, Menon S, Xiang Y. Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications. GENE REGULATION AND SYSTEMS BIOLOGY 2016; 10:51-66. [PMID: 27429547 PMCID: PMC4944831 DOI: 10.4137/grsb.s39076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/31/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022]
Abstract
Biological network models offer a framework for understanding disease by describing the relationships between the mechanisms involved in the regulation of biological processes. Crowdsourcing can efficiently gather feedback from a wide audience with varying expertise. In the Network Verification Challenge, scientists verified and enhanced a set of 46 biological networks relevant to lung and chronic obstructive pulmonary disease. The networks were built using Biological Expression Language and contain detailed information for each node and edge, including supporting evidence from the literature. Network scoring of public transcriptomics data inferred perturbation of a subset of mechanisms and networks that matched the measured outcomes. These results, based on a computable network approach, can be used to identify novel mechanisms activated in disease, quantitatively compare different treatments and time points, and allow for assessment of data with low signal. These networks are periodically verified by the crowd to maintain an up-to-date suite of networks for toxicology and drug discovery applications.
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Affiliation(s)
| | - Aishwarya Alex Namasivayam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | | | | | - Aravind Tallam
- TWINCORE, Zentrum für Experimentelle und Klinische Infektionsforschung, Hannover, Germany
| | | | | | - Dheeraj Reddy Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | - Ganna Androsova
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Irina Shvydchenko
- Kuban State University of Physical Education, Sport and Tourism, Krasnodar, Russia
| | | | - Jorge Val Calvo
- Center for Molecular Biology, “Severo Ochoa” – Spanish National Research Council, Madrid, Spain
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | - Manuel C. Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | | | - Maria Biryukov
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | | | - Neha Rohatgi
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | | | - Rajesh Mandarapu
- Prakhya Research Laboratories, Lakshminagar, Selaiyur, Chennai, Tamil Nadu, India
| | | | - Sergey Davidyan
- Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russia
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | - Svetlana Guryanova
- Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, Russia
| | - Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Swapna Menon
- AnalyzeDat Consulting Services, Edapally Byepass Junction, Kochi, Kerala, India
| | - Yang Xiang
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
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21
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Rinaldi F, Ellendorff TR, Madan S, Clematide S, van der Lek A, Mevissen T, Fluck J. BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw067. [PMID: 27402677 PMCID: PMC4940434 DOI: 10.1093/database/baw067] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/11/2016] [Indexed: 12/27/2022]
Abstract
Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and medical text mining. Track 4 at BioCreative V attempts to approach this complexity using fragments of large-scale manually curated biological networks, represented in Biological Expression Language (BEL), as training and test data. BEL is an advanced knowledge representation format which has been designed to be both human readable and machine processable. The specific goal of track 4 was to evaluate text mining systems capable of automatically constructing BEL statements from given evidence text, and of retrieving evidence text for given BEL statements. Given the complexity of the task, we designed an evaluation methodology which gives credit to partially correct statements. We identified various levels of information expressed by BEL statements, such as entities, functions, relations, and introduced an evaluation framework which rewards systems capable of delivering useful BEL fragments at each of these levels. The aim of this evaluation method is to help identify the characteristics of the systems which, if combined, would be most useful for achieving the overall goal of automatically constructing causal biological networks from text.
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Affiliation(s)
- Fabio Rinaldi
- Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland
| | | | - Sumit Madan
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany
| | - Simon Clematide
- Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland
| | - Adrian van der Lek
- Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland
| | - Theo Mevissen
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany
| | - Juliane Fluck
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany
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22
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Lopez-Campos JL, Calero-Acuña C, Lopez-Ramirez C, Abad-Arranz M, Márquez-Martín E, Ortega-Ruiz F, Arellano E. Implications of the inflammatory response for the identification of biomarkers of chronic obstructive pulmonary disease. Biomark Med 2016; 10:109-22. [PMID: 26808692 DOI: 10.2217/bmm.15.87] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by both local and systemic inflammation. Because inflammation plays a critical role in the development, course and severity of COPD, inflammatory markers have the potential to improve the current diagnostic and prognostic approaches. Local inflammation in COPD is characterized by an infiltration of inflammatory cells, with an increased expression of cytokines, chemokines, enzymes, growth factors and adhesion molecules. Systemic low-grade inflammation is another common but nonspecific finding in COPD. Exacerbations of COPD are acute clinical events accompanied by an exaggerated inflammatory response. Future investigations in the field of COPD biomarkers should take into account different study designs and biochemical assays, disease course and duration, variations in symptom severity and timing of measurement.
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Affiliation(s)
- Jose Luis Lopez-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Calero-Acuña
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Cecilia Lopez-Ramirez
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - María Abad-Arranz
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - Eduardo Márquez-Martín
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - Francisco Ortega-Ruiz
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Arellano
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
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23
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Boue S, Fields B, Hoeng J, Park J, Peitsch MC, Schlage WK, Talikka M, Binenbaum I, Bondarenko V, Bulgakov OV, Cherkasova V, Diaz-Diaz N, Fedorova L, Guryanova S, Guzova J, Igorevna Koroleva G, Kozhemyakina E, Kumar R, Lavid N, Lu Q, Menon S, Ouliel Y, Peterson SC, Prokhorov A, Sanders E, Schrier S, Schwaitzer Neta G, Shvydchenko I, Tallam A, Villa-Fombuena G, Wu J, Yudkevich I, Zelikman M. Enhancement of COPD biological networks using a web-based collaboration interface. F1000Res 2015; 4:32. [PMID: 25767696 PMCID: PMC4350443 DOI: 10.12688/f1000research.5984.2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/14/2015] [Indexed: 01/06/2023] Open
Abstract
The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website ( https://bionet.sbvimprover.com/) and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD-relevant models that can be used to help understand the mechanisms related to lung pathobiology. Registered users of the website can freely browse and download the networks.
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Affiliation(s)
- The sbv IMPROVER project team (in alphabetical order)
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
- Private, Washington DC, USA
- USAMRIID, Attn: MCMR-UIZ-R, 1425 Porter Street, Frederick, MD, 21702-5011, USA
- Private, Boston, MA, USA
- Institute of Microbial Technology, Chandigarh, 160036, India
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
- AnalyzeDat Consulting Services, Ernakulam, India
- Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
- Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| | - Stephanie Boue
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Brett Fields
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Jennifer Park
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
| | - Manuel C. Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Walter K. Schlage
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - The Challenge Best Performers (in alphabetical order)
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
- Private, Washington DC, USA
- USAMRIID, Attn: MCMR-UIZ-R, 1425 Porter Street, Frederick, MD, 21702-5011, USA
- Private, Boston, MA, USA
- Institute of Microbial Technology, Chandigarh, 160036, India
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
- AnalyzeDat Consulting Services, Ernakulam, India
- Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
- Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| | - Ilona Binenbaum
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
| | - Vladimir Bondarenko
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
| | - Oleg V. Bulgakov
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
| | | | - Norberto Diaz-Diaz
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
| | - Larisa Fedorova
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
| | - Svetlana Guryanova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | | | | | | | - Rahul Kumar
- Institute of Microbial Technology, Chandigarh, 160036, India
| | - Noa Lavid
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | - Qingxian Lu
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
| | - Swapna Menon
- AnalyzeDat Consulting Services, Ernakulam, India
| | - Yael Ouliel
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | | | - Alexander Prokhorov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | - Edward Sanders
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
| | - Sarah Schrier
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | | | - Irina Shvydchenko
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
| | - Aravind Tallam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
| | | | - John Wu
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
| | - Ilya Yudkevich
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
| | - Mariya Zelikman
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
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24
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Boue S, Fields B, Hoeng J, Park J, Peitsch MC, Schlage WK, Talikka M, Binenbaum I, Bondarenko V, Bulgakov OV, Cherkasova V, Diaz-Diaz N, Fedorova L, Guryanova S, Guzova J, Igorevna Koroleva G, Kozhemyakina E, Kumar R, Lavid N, Lu Q, Menon S, Ouliel Y, Peterson SC, Prokhorov A, Sanders E, Schrier S, Schwaitzer Neta G, Shvydchenko I, Tallam A, Villa-Fombuena G, Wu J, Yudkevich I, Zelikman M. Enhancement of COPD biological networks using a web-based collaboration interface. F1000Res 2015; 4:32. [PMID: 25767696 PMCID: PMC4350443 DOI: 10.12688/f1000research.5984.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2015] [Indexed: 11/20/2022] Open
Abstract
The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website ( https://bionet.sbvimprover.com/) and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD-relevant models that can be used to help understand the mechanisms related to lung pathobiology. Registered users of the website can freely browse and download the networks.
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Affiliation(s)
- The sbv IMPROVER project team (in alphabetical order)
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
- Private, Washington DC, USA
- USAMRIID, Attn: MCMR-UIZ-R, 1425 Porter Street, Frederick, MD, 21702-5011, USA
- Private, Boston, MA, USA
- Institute of Microbial Technology, Chandigarh, 160036, India
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
- AnalyzeDat Consulting Services, Ernakulam, India
- Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
- Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| | - Stephanie Boue
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Brett Fields
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Jennifer Park
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
| | - Manuel C. Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Walter K. Schlage
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - The Challenge Best Performers (in alphabetical order)
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- Selventa, One Alewife Center, Cambridge, MA, 02140, USA
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
- Private, Washington DC, USA
- USAMRIID, Attn: MCMR-UIZ-R, 1425 Porter Street, Frederick, MD, 21702-5011, USA
- Private, Boston, MA, USA
- Institute of Microbial Technology, Chandigarh, 160036, India
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
- AnalyzeDat Consulting Services, Ernakulam, India
- Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
- Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
| | - Ilona Binenbaum
- Systems Bioengineering Group - National Technical University of Athens, Ethniko Metsovio Politechnio, , 28is Oktovriou 42, Athina, 106 82, Greece
| | - Vladimir Bondarenko
- Touro University Nevada, 874 American Pacific Drive, Henderson, NV, 89052, USA
| | - Oleg V. Bulgakov
- University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA, 15260, USA
| | | | - Norberto Diaz-Diaz
- Intelligent Data Analysis Group (DATAi), School of Engineering, Pablo de Olavide University, Ctra. de Utrera, km. 1 41013, Sevilla, Spain
| | - Larisa Fedorova
- University of Toledo, 2801 W Bancroft St, Toledo, OH, 43606, USA
| | - Svetlana Guryanova
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | | | | | | | - Rahul Kumar
- Institute of Microbial Technology, Chandigarh, 160036, India
| | - Noa Lavid
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | - Qingxian Lu
- Louisville University, 301 E. Muhammad Ali Blvd, Louisville, KY, 40202, USA
| | - Swapna Menon
- AnalyzeDat Consulting Services, Ernakulam, India
| | - Yael Ouliel
- Technion - Israel Institute of Technology, Technion City, Haifa, 3200003, Israel
| | | | - Alexander Prokhorov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, 16/10, Miklukho-Maklay str., Moscow, 117997, Russian Federation
| | - Edward Sanders
- Edward Sanders Scientific Consulting, Rue du Clos 33, 2034 Peseux, Switzerland
| | - Sarah Schrier
- Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | | | - Irina Shvydchenko
- Kuban State University of Physical Education, Sport and Tourism, 161, Budennogo Str., Krasnodar City, 350015, Russian Federation
| | - Aravind Tallam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, 4362 Esch sur Alzette, Luxembourg
| | | | - John Wu
- Cal Biopharma, 710 Somerset Ln, Foster Cit, CA, 94404-3728, USA
| | - Ilya Yudkevich
- University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
| | - Mariya Zelikman
- University of Washington, 1959 NE Pacific Street, HSB T-466, Seattle, WA, USA
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