1
|
Seton KA, Espejo-Oltra JA, Giménez-Orenga K, Haagmans R, Ramadan DJ, Mehlsen J. Advancing Research and Treatment: An Overview of Clinical Trials in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Future Perspectives. J Clin Med 2024; 13:325. [PMID: 38256459 PMCID: PMC10816159 DOI: 10.3390/jcm13020325] [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: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic, debilitating, and multi-faceted illness. Heterogenous onset and clinical presentation with additional comorbidities make it difficult to diagnose, characterize, and successfully treat. Current treatment guidelines focus on symptom management, but with no clear target or causative mechanism, remission rates are low, and fewer than 5% of patients return to their pre-morbid activity levels. Therefore, there is an urgent need to undertake robust clinical trials to identify effective treatments. This review synthesizes insights from clinical trials exploring pharmacological interventions and dietary supplements targeting immunological, metabolic, gastrointestinal, neurological, and neuroendocrine dysfunction in ME/CFS patients which require further exploration. Additionally, the trialling of alternative interventions in ME/CFS based on reported efficacy in the treatment of illnesses with overlapping symptomology is also discussed. Finally, we provide important considerations and make recommendations, focusing on outcome measures, to ensure the execution of future high-quality clinical trials to establish clinical efficacy of evidence-based interventions that are needed for adoption in clinical practice.
Collapse
Affiliation(s)
- Katharine A. Seton
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK;
| | - José A. Espejo-Oltra
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany;
- Department of Pathology, School of Health Sciences, Universidad Católica de Valencia, San Vicente Mártir, 46001 Valencia, Spain
| | - Karen Giménez-Orenga
- Escuela de Doctorado, Universidad Católica de Valencia, San Vicente Mártir, 46001 Valencia, Spain;
| | - Rik Haagmans
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK;
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Donia J. Ramadan
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Kirkeveien 166, 0450 Oslo, Norway;
| | - Jesper Mehlsen
- Surgical Pathophysiology Unit, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark;
| |
Collapse
|
2
|
Chacko TP, Toole JT, Morris MC, Page J, Forsten RD, Barrett JP, Reinhard MJ, Brewster RC, Costanzo ME, Broderick G. A regulatory pathway model of neuropsychological disruption in Havana syndrome. Front Psychiatry 2023; 14:1180929. [PMID: 37965360 PMCID: PMC10642174 DOI: 10.3389/fpsyt.2023.1180929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/29/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction In 2016 diplomatic personnel serving in Havana, Cuba, began reporting audible sensory phenomena paired with onset of complex and persistent neurological symptoms consistent with brain injury. The etiology of these Anomalous Health Incidents (AHI) and subsequent symptoms remains unknown. This report investigates putative exposure-symptom pathology by assembling a network model of published bio-behavioral pathways and assessing how dysregulation of such pathways might explain loss of function in these subjects using data available in the published literature. Given similarities in presentation with mild traumatic brain injury (mTBI), we used the latter as a clinically relevant means of evaluating if the neuropsychological profiles observed in Havana Syndrome Havana Syndrome might be explained at least in part by a dysregulation of neurotransmission, neuro-inflammation, or both. Method Automated text-mining of >9,000 publications produced a network consisting of 273 documented regulatory interactions linking 29 neuro-chemical markers with 9 neuropsychological constructs from the Brief Mood Survey, PTSD Checklist, and the Frontal Systems Behavior Scale. Analysis of information flow through this network produced a set of regulatory rules reconciling to within a 6% departure known mechanistic pathways with neuropsychological profiles in N = 6 subjects. Results Predicted expression of neuro-chemical markers that jointly satisfy documented pathways and observed symptom profiles display characteristically elevated IL-1B, IL-10, NGF, and norepinephrine levels in the context of depressed BDNF, GDNF, IGF1, and glutamate expression (FDR < 5%). Elevations in CRH and IL-6 were also predicted unanimously across all subjects. Furthermore, simulations of neurological regulatory dynamics reveal subjects do not appear to be "locked in" persistent illness but rather appear to be engaged in a slow recovery trajectory. Discussion This computational analysis of measured neuropsychological symptoms in Havana-based diplomats proposes that these AHI symptoms may be supported in part by disruption of known neuroimmune and neurotransmission regulatory mechanisms also associated with mTBI.
Collapse
Affiliation(s)
- Thomas P. Chacko
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - J. Tory Toole
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - Matthew C. Morris
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - Jeffrey Page
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - Robert D. Forsten
- War Related Illness and Injury Study Center (WRIISC), Department of Veterans Affairs, Washington, DC, United States
| | - John P. Barrett
- War Related Illness and Injury Study Center (WRIISC), Department of Veterans Affairs, Washington, DC, United States
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, MD, United States
| | - Matthew J. Reinhard
- War Related Illness and Injury Study Center (WRIISC), Department of Veterans Affairs, Washington, DC, United States
- Complex Exposures Threats Center, Department of Veterans Affairs, Washington, DC, United States
| | - Ryan C. Brewster
- War Related Illness and Injury Study Center (WRIISC), Department of Veterans Affairs, Washington, DC, United States
| | - Michelle E. Costanzo
- War Related Illness and Injury Study Center (WRIISC), Department of Veterans Affairs, Washington, DC, United States
- Complex Exposures Threats Center, Department of Veterans Affairs, Washington, DC, United States
- Department of Medicine, Uniformed Services University, Bethesda, MD, United States
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
- Complex Exposures Threats Center, Department of Veterans Affairs, Washington, DC, United States
| |
Collapse
|
3
|
Old drugs, new tricks: leveraging known compounds to disrupt coronavirus-induced cytokine storm. NPJ Syst Biol Appl 2022; 8:38. [PMID: 36216820 PMCID: PMC9549818 DOI: 10.1038/s41540-022-00250-9] [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: 02/04/2022] [Accepted: 09/27/2022] [Indexed: 11/11/2022] Open
Abstract
A major complication in COVID-19 infection consists in the onset of acute respiratory distress fueled by a dysregulation of the host immune network that leads to a run-away cytokine storm. Here, we present an in silico approach that captures the host immune system’s complex regulatory dynamics, allowing us to identify and rank candidate drugs and drug pairs that engage with minimal subsets of immune mediators such that their downstream interactions effectively disrupt the signaling cascades driving cytokine storm. Drug–target regulatory interactions are extracted from peer-reviewed literature using automated text-mining for over 5000 compounds associated with COVID-induced cytokine storm and elements of the underlying biology. The targets and mode of action of each compound, as well as combinations of compounds, were scored against their functional alignment with sets of competing model-predicted optimal intervention strategies, as well as the availability of like-acting compounds and known off-target effects. Top-ranking individual compounds identified included a number of known immune suppressors such as calcineurin and mTOR inhibitors as well as compounds less frequently associated for their immune-modulatory effects, including antimicrobials, statins, and cholinergic agonists. Pairwise combinations of drugs targeting distinct biological pathways tended to perform significantly better than single drugs with dexamethasone emerging as a frequent high-ranking companion. While these predicted drug combinations aim to disrupt COVID-induced acute respiratory distress syndrome, the approach itself can be applied more broadly to other diseases and may provide a standard tool for drug discovery initiatives in evaluating alternative targets and repurposing approved drugs.
Collapse
|
4
|
Improvement of the Public Health Service Platform System Based on the Big Data-Driven System. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:1476779. [PMID: 35845906 PMCID: PMC9279029 DOI: 10.1155/2022/1476779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022]
Abstract
At present, complex discrete dynamic systems are widely used in the field of medicine. The control system in the complex discrete dynamic model is gradually transformed into intelligent control. It has become the main research direction of researchers to improve the medical platform system by adding different modeling strategies. The traditional discrete modeling technology can only be used as the knowledge content of students' textbooks because it can no longer meet the needs of the development of human society. In order to improve the application of a discrete system in the public platform, this paper studies the improvement of the public health service platform system based on the complex discrete dynamic system. Firstly, a time-driven control strategy is proposed to study the output feedback control with random sampling in the platform. Then, the stability of random parameters and the addition of dynamic scheduling strategies are further studied. Compared with the traditional system, the optimized system greatly strengthens the data transmission problem of input and output channels. The results show that by improving the performance of the public health service platform system, the probability of problems in the process of data transmission is greatly reduced. After adding controllable and observable performance to the system, the stability of the whole system is further improved. The improved public health service platform system studied in this paper can store and transmit a large number of user data in the network environment, automatically maintaining the stability of the system and has a good social application value.
Collapse
|
5
|
Shinn EH, Busch BE, Jasemi N, Lyman CA, Toole JT, Richman SC, Symmans WF, Chavez-MacGregor M, Peterson SK, Broderick G. Network Modeling of Complex Time-Dependent Changes in Patient Adherence to Adjuvant Endocrine Treatment in ER+ Breast Cancer. Front Psychol 2022; 13:856813. [PMID: 35903747 PMCID: PMC9315289 DOI: 10.3389/fpsyg.2022.856813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022] Open
Abstract
Early patient discontinuation from adjuvant endocrine treatment (ET) is multifactorial and complex: Patients must adapt to various challenges and make the best decisions they can within changing contexts over time. Predictive models are needed that can account for the changing influence of multiple factors over time as well as decisional uncertainty due to incomplete data. AtlasTi8 analyses of longitudinal interview data from 82 estrogen receptor-positive (ER+) breast cancer patients generated a model conceptualizing patient-, patient-provider relationship, and treatment-related influences on early discontinuation. Prospective self-report data from validated psychometric measures were discretized and constrained into a decisional logic network to refine and validate the conceptual model. Minimal intervention set (MIS) optimization identified parsimonious intervention strategies that reversed discontinuation paths back to adherence. Logic network simulation produced 96 candidate decisional models which accounted for 75% of the coordinated changes in the 16 network nodes over time. Collectively the models supported 15 persistent end-states, all discontinued. The 15 end-states were characterized by median levels of general anxiety and low levels of perceived recurrence risk, quality of life (QoL) and ET side effects. MIS optimization identified 3 effective interventions: reducing general anxiety, reinforcing pill-taking routines, and increasing trust in healthcare providers. Increasing health literacy also improved adherence for patients without a college degree. Given complex regulatory networks’ intractability to end-state identification, the predictive models performed reasonably well in identifying specific discontinuation profiles and potentially effective interventions.
Collapse
Affiliation(s)
- Eileen H. Shinn
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- *Correspondence: Eileen H. Shinn,
| | - Brooke E. Busch
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Neda Jasemi
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Cole A. Lyman
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - J. Tory Toole
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - Spencer C. Richman
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - William Fraser Symmans
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mariana Chavez-MacGregor
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Susan K. Peterson
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| |
Collapse
|
6
|
Stanculescu D, Bergquist J. Perspective: Drawing on Findings From Critical Illness to Explain Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Front Med (Lausanne) 2022; 9:818728. [PMID: 35345768 PMCID: PMC8957276 DOI: 10.3389/fmed.2022.818728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/11/2022] [Indexed: 12/15/2022] Open
Abstract
We propose an initial explanation for how myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) could originate and perpetuate by drawing on findings from critical illness research. Specifically, we combine emerging findings regarding (a) hypoperfusion and endotheliopathy, and (b) intestinal injury in these illnesses with our previously published hypothesis about the role of (c) pituitary suppression, and (d) low thyroid hormone function associated with redox imbalance in ME/CFS. Moreover, we describe interlinkages between these pathophysiological mechanisms as well as “vicious cycles” involving cytokines and inflammation that may contribute to explain the chronic nature of these illnesses. This paper summarizes and expands on our previous publications about the relevance of findings from critical illness for ME/CFS. New knowledge on diagnostics, prognostics and treatment strategies could be gained through active collaboration between critical illness and ME/CFS researchers, which could lead to improved outcomes for both conditions.
Collapse
Affiliation(s)
| | - Jonas Bergquist
- Division of Analytical Chemistry and Neurochemistry, Department of Chemistry - Biomedical Center, Uppsala University, Uppsala, Sweden.,The Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) Collaborative Research Centre at Uppsala University, Uppsala, Sweden
| |
Collapse
|
7
|
Stanculescu D, Larsson L, Bergquist J. Theory: Treatments for Prolonged ICU Patients May Provide New Therapeutic Avenues for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Front Med (Lausanne) 2021; 8:672370. [PMID: 34026797 PMCID: PMC8137963 DOI: 10.3389/fmed.2021.672370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
We here provide an overview of treatment trials for prolonged intensive care unit (ICU) patients and theorize about their relevance for potential treatment of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Specifically, these treatment trials generally target: (a) the correction of suppressed endocrine axes, notably through a "reactivation" of the pituitary gland's pulsatile secretion of tropic hormones, or (b) the interruption of the "vicious circle" between inflammation, oxidative and nitrosative stress (O&NS), and low thyroid hormone function. There are significant parallels in the treatment trials for prolonged critical illness and ME/CFS; this is consistent with the hypothesis of an overlap in the mechanisms that prevent recovery in both conditions. Early successes in the simultaneous reactivation of pulsatile pituitary secretions in ICU patients-and the resulting positive metabolic effects-could indicate an avenue for treating ME/CFS. The therapeutic effects of thyroid hormones-including in mitigating O&NS and inflammation and in stimulating the adreno-cortical axis-also merit further studies. Collaborative research projects should further investigate the lessons from treatment trials for prolonged critical illness for solving ME/CFS.
Collapse
Affiliation(s)
| | - Lars Larsson
- Basic and Clinical Muscle Biology, Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - Jonas Bergquist
- Analytical Chemistry and Neurochemistry, Department of Chemistry–Biomedical Center, Uppsala University, Uppsala, Sweden
- The Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) Collaborative Research Centre at Uppsala University, Uppsala, Sweden
| |
Collapse
|
8
|
Stanculescu D, Larsson L, Bergquist J. Hypothesis: Mechanisms That Prevent Recovery in Prolonged ICU Patients Also Underlie Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Front Med (Lausanne) 2021; 8:628029. [PMID: 33585528 PMCID: PMC7876311 DOI: 10.3389/fmed.2021.628029] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Here the hypothesis is advanced that maladaptive mechanisms that prevent recovery in some intensive care unit (ICU) patients may also underlie Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Specifically, these mechanisms are: (a) suppression of the pituitary gland's pulsatile secretion of tropic hormones, and (b) a "vicious circle" between inflammation, oxidative and nitrosative stress (O&NS), and low thyroid hormone function. This hypothesis should be investigated through collaborative research projects.
Collapse
Affiliation(s)
| | - Lars Larsson
- Basic and Clinical Muscle Biology, Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - Jonas Bergquist
- Analytical Chemistry and Neurochemistry, Department of Chemistry – Biomedical Center, Uppsala University, Uppsala, Sweden
- The Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) Collaborative Research Centre at Uppsala University, Uppsala, Sweden
| |
Collapse
|
9
|
Morris MC, Chapman TJ, Pichichero ME, Broderick G. Immune Network Modeling Predicts Specific Nasopharyngeal and Peripheral Immune Dysregulation in Otitis-Prone Children. Front Immunol 2020; 11:1168. [PMID: 32595639 PMCID: PMC7301607 DOI: 10.3389/fimmu.2020.01168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 05/12/2020] [Indexed: 11/18/2022] Open
Abstract
Acute otitis media (AOM) pathogenesis involves nasopharyngeal colonization by potential otopathogens and a viral co-infection. Stringently-defined otitis prone (sOP) children show characteristic patterns of immune dysfunction. We hypothesized that otitis proneness is largely a result of altered signaling between immune components that are otherwise competent, resulting in increased susceptibility to infection by bacterial otopathogens. To test this, we constructed a regulatory immune network model linking immune cells and signaling elements known to be involved in AOM and/or dysregulated in sOP children. The alignment of immune response mechanisms with data from in vivo and in vitro experimental observations produced 82 putative immune network models, each describing variants of immune regulatory networks consistent with available observations. Analysis of these models suggested that new measurements of serum levels of IL-4 and CXCL8 could refine competing models and resulted in the elimination of 38 of the models. Further analysis of the remaining 44 models suggested specific deviations in the predicted regulation of nasopharyngeal and peripheral immunity during response to AOM. Specifically, immune responses active in sOP children during AOM were characterized by early and constitutive activation of pro-inflammatory signaling in the nasopharynx and a Th2- and Treg-dominated profile in the periphery. We conclude that sOP children have altered regulation of key immune mediators during both health and pathogenesis. This altered regulation may be amenable to therapeutic intervention.
Collapse
Affiliation(s)
- Matthew C. Morris
- Center for Clinical Systems Biology, Research Institute, Rochester General Hospital, Rochester, NY, United States
| | - Timothy J. Chapman
- Center for Infectious Diseases and Immunology, Research Institute, Rochester General Hospital, Rochester, NY, United States
| | - Michael E. Pichichero
- Center for Infectious Diseases and Immunology, Research Institute, Rochester General Hospital, Rochester, NY, United States
| | - Gordon Broderick
- Center for Clinical Systems Biology, Research Institute, Rochester General Hospital, Rochester, NY, United States
- Department of Biomedical Engineering, Rochester Institute of Technology, Rochester, NY, United States
| |
Collapse
|
10
|
Sedghamiz H, Morris M, Craddock TJA, Whitley D, Broderick G. Bio-ModelChecker: Using Bounded Constraint Satisfaction to Seamlessly Integrate Observed Behavior With Prior Knowledge of Biological Networks. Front Bioeng Biotechnol 2019; 7:48. [PMID: 30972331 PMCID: PMC6443719 DOI: 10.3389/fbioe.2019.00048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/28/2019] [Indexed: 01/31/2023] Open
Abstract
The in silico study and reverse engineering of regulatory networks has gained in recognition as an insightful tool for the qualitative study of biological mechanisms that underlie a broad range of complex illness. In the creation of reliable network models, the integration of prior mechanistic knowledge with experimentally observed behavior is hampered by the disparate nature and widespread sparsity of such measurements. The former challenges conventional regression-based parameter fitting while the latter leads to large sets of highly variable network models that are equally compliant with the data. In this paper, we propose a bounded Constraint Satisfaction (CS) based model checking framework for parameter set identification that readily accommodates partial records and the exponential complexity of this problem. We introduce specific criteria to describe the biological plausibility of competing multi-valued regulatory networks that satisfy all the constraints and formulate model identification as a multi-objective optimization problem. Optimization is directed at maximizing structural parsimony of the regulatory network by mitigating excessive control action selectivity while also favoring increased state transition efficiency and robustness of the network's dynamic response. The framework's scalability, computational time and validity is demonstrated on several well-established and well-studied biological networks.
Collapse
Affiliation(s)
- Hooman Sedghamiz
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - Matthew Morris
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
| | - Travis J. A Craddock
- Institute for Neuro Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
- Departments of Psychology and Neuroscience, Computer Science, and Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Darrell Whitley
- School of Computer Science, Colorado State University, Fort Collins, CO, United States
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY, United States
- Department of Biomedical Engineering, Rochester Institute of Technology, Rochester, NY, United States
| |
Collapse
|
11
|
Sedghamiz H, Morris M, Whitley D, Craddock TJA, Pichichero M, Broderick G. Computation of Robust Minimal Intervention Sets in Multi-Valued Biological Regulatory Networks. Front Physiol 2019; 10:241. [PMID: 30941053 PMCID: PMC6433979 DOI: 10.3389/fphys.2019.00241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/25/2019] [Indexed: 02/06/2023] Open
Abstract
Enabled by rapid advances in computational sciences, in silico logical modeling of complex and large biological networks is more and more feasible making it an increasingly popular approach among biologists. Automated high-throughput, drug target identification is one of the primary goals of this in silico network biology. Targets identified in this way are then used to mine a library of drug chemical compounds in order to identify appropriate therapies. While identification of drug targets is exhaustively feasible on small networks, it remains computationally difficult on moderate and larger models. Moreover, there are several important constraints such as off-target effects, efficacy and safety that should be integrated into the identification of targets if the intention is translation to the clinical space. Here we introduce numerical constraints whereby efficacy is represented by efficiency in response and robustness of outcome. This paper introduces an algorithm that relies on a Constraint Satisfaction (CS) technique to efficiently compute the Minimal Intervention Sets (MIS) within a set of often complex clinical safety constraints with the aim of identifying the smallest least invasive set of targets pharmacologically accessible for therapy that most efficiently and reliably achieve the desired outcome.
Collapse
Affiliation(s)
- Hooman Sedghamiz
- Center for Clinical Systems Biology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Matthew Morris
- Center for Clinical Systems Biology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Darrell Whitley
- School of Computer Science, Colorado State University, Fort Collins, CO, United States
| | - Travis J A Craddock
- Department of Psychology and Neuroscience, Nova Southeastern University, Fort Lauderdale, FL, United States.,Department of Computer Science, Nova Southeastern University, Fort Lauderdale, FL, United States.,Department of Clinical Immunology, Nova Southeastern University, Fort Lauderdale, FL, United States.,Clinical Systems Biology Group, Institute for NeuroImmune Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Michael Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital Research Institute, Rochester, NY, United States.,Department of Biomedical Engineering, Rochester Institute of Technology, Rochester, NY, United States
| |
Collapse
|