Systematic data capture reduces the need for source data verification: exploratory analysis from a phase 2 multicenter randomized controlled platform trial

Communications Medicine · 2025-10-29

BACKGROUND: The COVID-19 pandemic gave rise to clinical trials focused on systematic, accurate primary data capture, and reduced reliance on source data verification (SDV). Here, we report on a natural experiment that allowed us to assess the quality, cost, and impact of this approach compared to traditional SDV. METHODS: The I-SPY COVID trial (NCT04488081) was a multicenter, open-label, platform trial that employed a streamlined daily checklist, daily capture of labs and medications, and centralized monitoring to ensure accurate data collection in lieu of SDV. The trial enrolled 1,111 patients in 11 drug arms with severe COVID-19. After the trial arms were closed, extensive retrospective SDV was performed on 333 (30.0%) patients, including 10,101 of 44,486 (23%) electronic case report forms (eCRFs), allowing us to evaluate the impact of our strategy on data integrity, outcomes, and costs. RESULTS: We find that retrospective SDV results in changes to 0.36% (1,234 / 340,532) of data fields. It results in no changes to the type of outcome recorded (death, recovery, or censored), but changes in the day of recovery in 9 instances, by a median of 2 days (range 1-7). Two additional AEs are added during SDV that had not previously been captured. Costs associated with retrospective SDV of 23% eCRFs are 61,073 person-hours at a cost of $6.1 M. CONCLUSIONS: Extensive SDV does not change any results or conclusions of the I-SPY COVID trial, which was designed with a systematic strategy for data capture, monitoring, and safety. This strategy could improve the efficiency of clinical trials and eliminate the need for manual SDV.

Wildfire Smoke Exposure During COVID-19 Vaccination is Correlated with Reduced Humoral Immunity After Six Months

Journal of Allergy and Clinical Immunology · 2025-02-01

Circulating IL-13+ IL-17+ Inflammatory ILC2s Denote Severe Eosinophilic and Neutrophilic in Asthma

American Journal of Respiratory and Critical Care Medicine · 2025-05-01

Abstract Rationale: Approximately half of asthma patients present with severe neutrophilic inflammation, for which biomarkers are limited and therapeutic response is poor. IL-17A involvement has been identified as a major pathogenic player, and can promote glucocorticoid resistance. Group 2 innate lymphoid cells (ILC2s) are elevated in circulation blood and bronchoalveolar lavage (BAL) of asthmatics. These cells are prominent source of T2 cytokines. ILC produce a variety of cytokines, and while canonical ILC2s do not secrete IL-17A, plasticity of ILC cytokine secretion profile has been reported. The mechanisms and significance of ILC2s and their role in pathogenic cytokine production is not well understood. To understand the role of ILC2s, Ozone (O3) exposure was utilized to model ILC2-dependent airway hyperreactivity in response to oxidative stress. Methods: Methacholine (MCh) responsiveness, bronchoalveolar lavage (BAL), and circulating immune cells were characterized in a cohort of rhesus macaques with established airway hyperreactivity, housed at the California National Primate Research Center. Macaques were exposed to 0.3 ppm O3 for 6.5 hours, with lung function measured 8 hours and necropsy 42 hours post-O3 respectively. Baseline measurements were taken one week prior to O3 exposure. Techniques included methacholine challenge, flow cytometry, rtPCR, and Luminex®. Half of the cohort (n=6) received anti-oxidant treatment before O3 exposure, controlled for in post-O3 classification. All procedures were conducted with approval of the University of California, Davis Institutional Animal Cares and Use Committee. Results: In rhesus macaques, O3 exposure induced increased populations of neutrophils, eosinophils, and ILC2s, but not ILC3s, in the BAL, compared to baseline. Expression of Il17a in ILC2s was observed and correlated significantly with canonical ILC2 markers Gata3 and Il13, and Il22. Il17 and Il22 are typically produced by ILC3s, suggesting ILC2 plasticity. ILC2 Il17a expression was used to rank the monkeys into high (inflammatory ILC2s iILC2s), and low natural ILC2s (nILC2s) expressors. ILC2 Il17a was significantly correlated with reduced lung function (EC150) in the iILC2 group when compared with nILC2 macaques (p<0.05). Conclusions: The presence of iILC2s in macaques with reduced lung function following O3 exposure indicates that production of IL-17 by ILC2s specifically may be clinically significant in asthma patients and are a potential therapeutic target in cases of glucocorticoid resistance. Moreover, IL17+ILC2s hold potential as a biomarker in asthma, particularly in low T-2 asthma that currently lacks reliable biomarkers.

Investigating Asthma After Coccidioidomycosis Among Patients With Commercial Health Insurance, United States, 2017–2022

Mycoses · 2025-02-01 · 2 citations

ABSTRACT Background The relationship between asthma and coccidioidomycosis has not been fully described. We have hypothesised that Coccidioides could trigger inflammatory airway responses, similar to other fungi. Objectives: To estimate the frequency of new‐onset asthma‐related symptoms after coccidioidomycosis and identify potentially associated factors. Patients/Methods We used a large health insurance claims database to identify patients with coccidiomycosis with and without an asthma diagnosis code or a short‐acting β 2 agonist prescription in the year after diagnosis. Results Thirteen per cent of 1657 patients with an asthma diagnosis code or a short‐acting β 2 agonist prescription (median 2.5 months later). Conclusions Increased healthcare provider awareness of asthma as a potential coccidioidomycosis complication could benefit patients, especially female patients and patients with severe pulmonary infection.

Low TET1 Expression Levels in COPD Are Associated With High Numbers of Neutrophils and Surfactant Protein Serum Leakage

American Journal of Respiratory and Critical Care Medicine · 2025-05-01

Abstract Rationale: Emerging evidence supports that epigenetic dysregulation, specifically variations in DNA methylation, is implicated in chronic obstructive pulmonary disease (COPD). Genes related to oxidative stress, mucus production, and epithelial barrier integrity are under strong epigenetic control. Ten-eleven translocation (TET) proteins, known to catalyze the hydroxylation of 5-methylcytosine to 5-hydroxymethylcytosine, may play a significant role but their specific functions in COPD remain underexplored. We aimed to examine the relationship between TET gene expression and COPD clinical phenotypes, with a focus on inflammatory parameters. Methods: RNA-seq data from peripheral blood samples of former smoker COPD patients (n=17; 63-76 yrs old; 40% female) and healthy controls (n=15; 37-43 yrs old, 50% female) was evaluated. Correlations between TET1, TET2, and TET3 expression and immune cell counts, lung function, and COPD severity markers were assessed. Logistic regression and causal inference analyses were used to explore potential associations of TET1 with COPD. Results: TET1 expression was significantly downregulated in peripheral blood mononuclear cells of COPD patients. TET1 showed significant negative correlations with neutrophil counts in sputum and blood as well as with serum SP-D levels, a biomarker linked to COPD severity. Logistic regression indicated that higher TET1 expression was associated with reduced odds of COPD (OR=0.5201). In contrast, blood TET2 and TET3 were positively associated with neutrophil levels, and TET2 was inversely correlated with lung function (FEV1/FVC ratio). Causal inference analysis suggested that TET1's protective effect might be mediated through regulation of neutrophil levels. Conclusion: Our findings highlight a potential protective role for TET1 in COPD through the regulation of neutrophil counts, and serum SP-D, key indicators of airway inflammation severity. TET2 and TET3 on the other hand, were positively associated with inflammatory markers and negatively associated with lung function in COPD. This study suggests that members of the TET family may differentially regulate airway inflammation and may serve as novel epigenetic therapeutic targets in COPD.

In Silico Binding of Computationally Folded Structures of Human Surfactant Protein D (hSP-D) to SARS-CoV-2 Spike Wild Type and ACE2 Show Low Likelihood of SP-D's Role in Blocking SARS-CoV-2 ACE2 Binding

American Journal of Respiratory and Critical Care Medicine · 2025-05-01

Abstract Rationale While human surfactant protein D (hSP-D) has been of immunological interest for its antiviral capabilities over at least the past two decades, there do not currently exist experimentally derived structural images that include all of hSP-D's amino acids of importance, especially the N-Acetylglucosamine (NAG) binding site at Asparagine amino acid site number 90 (ASN90). Computational folding methods have improved capability to take given amino acid sequences and derive potential 3D conformations. In this study, we evaluated the computationally bound structures of three different, computationally folded SP-D structures with SARS-CoV-2 Spike Wild Type (WT) (PDB: 6VSB) and dimerized ACE2 (PDB: 6M18) to the computational bound structure of the X-Ray fragment of hSP-D (PDB: 3DBZ) that exists in RCSB with SARS-CoV-2 Spike WT and X-Ray fragment of porcine SP-D (PDB: 6BBE), which has numerous NAG sites, with SARS-CoV-2 Spike WT. Methods We used the computational folding tools I-TASSER, AlphaFold, and ESMFold with the amino acid sequence for hSP-D to find top 3D conformers. Then, we used a variation of the Quantum Approximate Optimization Algorithm (QAOA) implemented with a maximum-sized cut (MaxCut) of a graph, called QAOA-MaxCut, that utilizes only a single, initial Trotter-Suzuki decomposition step (SETS), dubbed “SETS-QAOA-MaxCut”, to prune the protein structures. Penultimately, we used ZDOCK to complete protein binding. Lastly, we used SAMSON's Biological Verification tool to identify top clashes and contacts for the top complexes for each of our structures, and to visualize the protein complexes. Results Figure 1 shows that the additional N-Acetylglucosamine sites on porcine SP-D appeared to have allowed porcine SP-D to produce a higher ZDOCK score than hSP-D, and all other bound SP-D structures outperform the X-Ray hSP-D structure without the ASN90 site for SARS-CoV-2 Spike WT binding. However, SP-D produced after using I-TASSER appears to bind best to ACE2. Conclusion No SP-D conformation bound to ACE2 or to SARS-CoV-2 Spike WT with a higher ZDOCK Score than SARS-CoV-2 Spike WT bound to ACE2. Clearly, computational folding methods can lead to dramatically different protein structure models than their X-ray or other experimentally-derived counterparts. This would make sense, considering that all three methods used here (AlphaFold, I-TASSER, ESMFold) use data from other, similar structures to be able to derive high confidence structures, but do not necessarily detail molecular conformations or even stoichiometry for effective protein structure determinations.

Effect of IL-33 and type 2 polarizing cytokines on IFNγ expression in NK92 cells

Journal of Allergy and Clinical Immunology · 2025-02-01

Low TET1 Expression Levels in COPD Are Associated with Airway and Blood Neutrophilia

medRxiv · 2025-04-16

Epigenetic dysregulation, particularly DNA methylation variations, is implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). Ten-eleven translocation (TET) proteins (TET1, TET2, and TET3) regulate DNA methylation and gene transcription. Impaired TET1 expression was previously associated with airway inflammation and asthma. Here we investigated TET gene associations with COPD severity. We found that reduced TET1 expression in peripheral blood mononuclear cells was associated with higher sputum and blood neutrophil counts, decreased lung function and increased disease severity in patients. These findings support a potential protective role and warrant further mechanistic investigations into the actions of TET1 in COPD.

The Effects of Cyproheptadine on Severe COVID-19 From the I-SPY COVID Adaptive Platform Trial

CHEST Critical Care · 2025-08-06

<h3>Background</h3> Severe COVID-19 has been associated with hypercoagulability and platelet activation, which is known to result in excessive accumulation of serotonin. However, few studies have evaluated whether serotonergic blockade may improve clinical outcomes among those with COVID-19. <h3>Research Question</h3> Does cyproheptadine, an antiserotonergic drug most commonly used to treat serotonin syndrome, improve time to clinical recovery in patients with severe COVID-19? <h3>Study Design and Methods</h3> The Investigation of Serial Studies to Predict Your Therapeutic Response With Imaging and Molecular Analysis in COVID (I-SPY COVID) study is a phase 2, multicenter, adaptive, open-label randomized controlled trial designed to screen potential therapeutic agents rapidly to identify those with a high probability of improving outcomes for hospitalized critically ill patients with COVID-19. For this report, participants randomized to receive cyproheptadine 8 mg enterally every 8 hours for 10 days or until hospital discharge were compared with concurrently enrolled control patients who were treated with the standard of care regimen of dexamethasone and remdesivir and did not receive an investigational agent. Bayesian survival regression models were used to model the hazard functions for the 2 events of interest: (1) recovery (treating death as a competing event) and (2) overall death as a function of randomization arm and baseline COVID-19 level. <h3>Results</h3> From September through December 2021, 35 participants were randomized and consented to receive cyproheptadine and 61 concurrent control patients were eligible for analysis. At that point, futility criteria were met and the data monitoring committee halted further enrollment into the cyproheptadine arm. The posterior probability that cyproheptadine would increase the rate of recovery was 0.1% and the posterior probability that cyproheptadine would improve survival was 16.3%. <h3>Interpretation</h3> In an open-label phase 2 trial of adults critically ill with severe COVID-19, cyproheptadine did not improve recovery or survival compared with the standard of care. <h3>Clinical Trial Registration</h3> ClinicalTrials.gov; No.: NCT04488081; URL: www.clinicaltrials.gov

Environmental Oxidative Stress Impairs Splenocyte Metabolism in Rats Exposed to Traffic Related Air Pollution

American Journal of Respiratory and Critical Care Medicine · 2025-05-01

Abstract Rationale: Inhaled environmental pollutants may cause systemic chronic oxidative stress but the underlying mechanisms are poorly understood. At UC Davis, a novel exposure facility adjacent to a major freeway tunnel (Caldecott Tunnel) system was developed to provide a platform for real-world, near-roadway experimental traffic-related air pollution (TRAP) exposure studies. We aimed to investigate oxidative stress-induced changes in splenocytes collected from rat models exposed to TRAP. These animals were housed in the Caldecott Tunnel Exposure Facility from 1 month of age and were studied 32 weeks later. Control animals were exposed to filtered air in the same facility. We hypothesized that chronic inhalational TRAP exposure alters splenocyte function. Methods: Frozen splenocytes form filtered air and TRAP-exposed age-and sex-matched Fischer 344 rats (36 weeks of age) were thawed up and cultured in RPMI with L-glutamine, 10% FBS, and 1% penicillin-streptomycin, with or without stimulation by phorbol myristate acetate (PMA) and ionomycin. Cells were plated in 96-well plates at varying concentrations (0.1, 0.75, 2.0 and 4 million/mL). Freshly isolated splenocytes from filtered air and TRAP-exposed rats were similarly plated, stimulated PMA/ionomycin and exposed to 200 µM tert-butyl hydroperoxide (TBHP) for 3 hours to induce oxidative stress. Protein content was measured by the BCA assay. Viability was assessed using a Trypan blue exclusion assay at 24 and 48h. Alamar blue assay was performed to evaluate metabolic activity. Results: The viability of frozen splenocytes measured at 48h significantly varied between the culture conditions with the lowest (4.3%) seen in the PMA/ionomycin and TBHP stimulated TRAP-exposed cells and the highest (67%) observed in the unstimulated cells from the filtered air-exposed control animals. Cell counts did not differ significantly between control or TRAP-exposed freshly isolated/cultured splenocytes that were also 90%&amp;lt; viable. However, alamar blue assay in these cells revealed that splenocytes from TRAP-exposed rats had significantly lower metabolic activity than those from control rats (p&amp;lt;0.05, n=4) with metabolic activity of the TRAP-exposed, PMA/ionomycin stimulated cells treated with TBHP displaying the lowest levels. Decreased metabolic activity corresponded with increased total protein concentrations in these samples. Conclusions: TRAP-exposed rat splenocytes are more susceptible to TBHP-induced oxidative stress effects and display significantly altered cellular metabolism compared with filtered air-exposed cells. Our results suggest that chronic inhalational exposure to air pollution impairs immune cell metabolism.