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Küçükosmanoglu A, Scoarta S, Houweling M, Spinu N, Wijnands T, Geerdink N, Meskers C, Kanev GK, Kiewiet B, Kouwenhoven M, Noske D, Wurdinger T, Pouwer M, Wolff M, Westerman BA. A Real-world Toxicity Atlas Shows that Adverse Events of Combination Therapies Commonly Result in Additive Interactions. Clin Cancer Res 2024; 30:1685-1695. [PMID: 38597991 PMCID: PMC11016889 DOI: 10.1158/1078-0432.ccr-23-0914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/09/2023] [Accepted: 01/10/2024] [Indexed: 04/11/2024]
Abstract
PURPOSE Combination therapies are a promising approach for improving cancer treatment, but it is challenging to predict their resulting adverse events in a real-world setting. EXPERIMENTAL DESIGN We provide here a proof-of-concept study using 15 million patient records from the FDA Adverse Event Reporting System (FAERS). Complex adverse event frequencies of drugs or their combinations were visualized as heat maps onto a two-dimensional grid. Adverse event frequencies were shown as colors to assess the ratio between individual and combined drug effects. To capture these patterns, we trained a convolutional neural network (CNN) autoencoder using 7,300 single-drug heat maps. In addition, statistical synergy analyses were performed on the basis of BLISS independence or χ2 testing. RESULTS The trained CNN model was able to decode patterns, showing that adverse events occur in global rather than isolated and unique patterns. Patterns were not likely to be attributed to disease symptoms given their relatively limited contribution to drug-associated adverse events. Pattern recognition was validated using trial data from ClinicalTrials.gov and drug combination data. We examined the adverse event interactions of 140 drug combinations known to be avoided in the clinic and found that near all of them showed additive rather than synergistic interactions, also when assessed statistically. CONCLUSIONS Our study provides a framework for analyzing adverse events and suggests that adverse drug interactions commonly result in additive effects with a high level of overlap of adverse event patterns. These real-world insights may advance the implementation of new combination therapies in clinical practice.
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Affiliation(s)
- Asli Küçükosmanoglu
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Silvia Scoarta
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Megan Houweling
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Nicoleta Spinu
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Thomas Wijnands
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Niek Geerdink
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Carolien Meskers
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Georgi K. Kanev
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Bert Kiewiet
- SAS, Cary, North Carolina
- ITsPeople, Zaltbommel, the Netherlands
| | - Mathilde Kouwenhoven
- Department of Neurology, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - David Noske
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Tom Wurdinger
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | | | - Bart A. Westerman
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
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Delpiano L, Rodenburg LW, Burke M, Nelson G, Amatngalim GD, Beekman JM, Gray MA. Dynamic regulation of airway surface liquid pH by TMEM16A and SLC26A4 in cystic fibrosis nasal epithelia with rare mutations. Proc Natl Acad Sci U S A 2023; 120:e2307551120. [PMID: 37967223 PMCID: PMC10666107 DOI: 10.1073/pnas.2307551120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/28/2023] [Indexed: 11/17/2023] Open
Abstract
In cystic fibrosis (CF), defects in the CF transmembrane conductance regulator (CFTR) channel lead to an acidic airway surface liquid (ASL), which compromises innate defence mechanisms, predisposing to pulmonary failure. Restoring ASL pH is a potential therapy for people with CF, particularly for those who cannot benefit from current highly effective modulator therapy. However, we lack a comprehensive understanding of the complex mechanisms underlying ASL pH regulation. The calcium-activated chloride channel, TMEM16A, and the anion exchanger, SLC26A4, have been proposed as targets for restoring ASL pH, but current results are contradictory and often utilise nonphysiological conditions. To provide better evidence for a role of these two proteins in ASL pH homeostasis, we developed an efficient CRISPR-Cas9-based approach to knock-out (KO) relevant transporters in primary airway basal cells lacking CFTR and then measured dynamic changes in ASL pH under thin-film conditions in fully differentiated airway cultures, which better simulate the in vivo situation. Unexpectantly, we found that both proteins regulated steady-state as well as agonist-stimulated ASL pH, but only under inflammatory conditions. Furthermore, we identified two Food and Drug Administration (FDA)-approved drugs which raised ASL pH by activating SLC26A4. While we identified a role for SLC26A4 in fluid absorption, KO had no effect on cyclic adenosine monophosphate (cAMP)-stimulated fluid secretion in airway organoids. Overall, we have identified a role of TMEM16A in ASL pH homeostasis and shown that both TMEM16A and SLC26A4 could be important alternative targets for ASL pH therapy in CF, particularly for those people who do not produce any functional CFTR.
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Affiliation(s)
- Livia Delpiano
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lisa W Rodenburg
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of the European Reference Network-LUNG, Utrecht 3584 EA, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht 3584 CT, The Netherlands
| | - Matthew Burke
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Glyn Nelson
- Bioimaging Unit, Ageing Research Laboratories, Campus for Ageing and Vitality, Newcastle University, Newcastle Upon Tyne NE4 5PL, United Kingdom
| | - Gimano D Amatngalim
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of the European Reference Network-LUNG, Utrecht 3584 EA, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht 3584 CT, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of the European Reference Network-LUNG, Utrecht 3584 EA, The Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht 3584 CT, The Netherlands
- Centre for Living Technologies, Alliance Eindhoven University of Technology, Wageningen University and Research, Utrecht University, University Medical Center Utrecht, Utrecht 3584 CB, The Netherlands
| | - Michael A Gray
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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Sridhar A, Depla JA, Mulder LA, Karelehto E, Brouwer L, Kruiswijk L, Vieira de Sá R, Meijer A, Evers MM, van Kuppeveld FJM, Pajkrt D, Wolthers KC. Enterovirus D68 Infection in Human Primary Airway and Brain Organoids: No Additional Role for Heparan Sulfate Binding for Neurotropism. Microbiol Spectr 2022; 10:e0169422. [PMID: 36154279 PMCID: PMC9603061 DOI: 10.1128/spectrum.01694-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/09/2022] [Indexed: 12/31/2022] Open
Abstract
Enterovirus D68 (EV-D68) is an RNA virus that can cause outbreaks of acute flaccid paralysis (AFP), a polio-like disease. Before 2010, EV-D68 was a rare pathogen associated with mild respiratory symptoms, but the recent EV-D68 related increase in severe respiratory illness and outbreaks of AFP is not yet understood. An explanation for the rise in severe disease is that it may be due to changes in the viral genome resulting in neurotropism. In this regard, in addition to sialic acid, binding to heparan sulfate proteoglycans (HSPGs) has been identified as a feature for viral entry of some EV-D68 strains in cell lines. Studies in human primary organotypic cultures that recapitulate human physiology will address the relevance of these HSPG-binding mutations for EV-D68 infection in vivo. Therefore, in this work, we studied the replication and neurotropism of previously determined sialic acid-dependent and HSPG-dependent strains using primary human airway epithelial (HAE) cultures and induced human pluripotent stem cell (iPSC)-derived brain organoids. All three strains (B2/2042, B2/947, and A1/1348) used in this study infected HAE cultures and human brain organoids (shown for the first time). Receptor-blocking experiments in both cultures confirm that B2/2042 infection is solely dependent on sialic acid, while B2/947 and A1/1348 (HSPG to a lesser extent) binds to sialic acid and HSPG for cell entry. Our data suggest that HSPG-binding can be used by EV-D68 for entry in human physiological models but offers no advantage for EV-D68 infection of brain cells. IMPORTANCE Recent outbreaks of enterovirus D68, a nonpolio enterovirus, is associated with a serious neurological condition in young children, acute flaccid myelitis (AFM). As there is no antiviral treatment or vaccine available for EV-D68 it is important to better understand how EV-D68 causes AFM and why only recent outbreaks are associated with AFM. We investigated if a change in receptor usage of EV-D68 increases the virulence of EV-D68 in the airway or the central nervous system and thus could explain the increase in AFM cases. We studied this using physiologically relevant human airway epithelium and cerebral organoid cultures that are physiologically relevant human models. Our data suggest that heparan sulfate proteoglycans can be used by EV-D68 as an additional entry receptor in human physiological models but offers no advantage for EV-D68 infection of brain cells, and our data show the potential of these 46 innovative models for virology.
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Affiliation(s)
- Adithya Sridhar
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Department of Medical Microbiology, OrganoVIR Labs, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children’s Hospital Department of Pediatric Infectious Diseases, Amsterdam, The Netherlands
| | - Josse A. Depla
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Department of Medical Microbiology, OrganoVIR Labs, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children’s Hospital Department of Pediatric Infectious Diseases, Amsterdam, The Netherlands
- uniQure Biopharma B.V., Amsterdam, The Netherlands
| | - Lance A. Mulder
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Department of Medical Microbiology, OrganoVIR Labs, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children’s Hospital Department of Pediatric Infectious Diseases, Amsterdam, The Netherlands
| | - Eveliina Karelehto
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Department of Medical Microbiology, OrganoVIR Labs, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children’s Hospital Department of Pediatric Infectious Diseases, Amsterdam, The Netherlands
| | - Lieke Brouwer
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Department of Medical Microbiology, OrganoVIR Labs, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children’s Hospital Department of Pediatric Infectious Diseases, Amsterdam, The Netherlands
| | - Leonie Kruiswijk
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Department of Medical Microbiology, OrganoVIR Labs, Amsterdam, The Netherlands
| | | | - Adam Meijer
- National Institute for Public Health and Environment, Centre for Infectious Diseases Research and Laboratory Surveillance, Bilthoven, The Netherlands
| | | | - Frank J. M. van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dasja Pajkrt
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Department of Medical Microbiology, OrganoVIR Labs, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children’s Hospital Department of Pediatric Infectious Diseases, Amsterdam, The Netherlands
| | - Katja C. Wolthers
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Department of Medical Microbiology, OrganoVIR Labs, Amsterdam, The Netherlands
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