Michael Kabesch

Rationale: The role of DNA methylation (DNAm) markers in the upper-airway microbiome related to asthma exacerbations despite inhaled corticosteroid (ICS) treatment is unexplored. Objectives: To identify whole-blood DNAm markers associated with the upper-airway microbiome related to asthma exacerbations despite ICS treatment. Methods: We analyzed salivary, nasal, and pharyngeal microbiome in 242 asthma patients (GEMAS) for discovery. We tested associations between whole-blood DNAm at 703,505 CpGs and 21 exacerbation-related microbiome traits. Replication for the nasal microbiome was evaluated in 272 (Project Viva) and 66 (SysPharmPediA) children with and without asthma. We analyzed differentially methylated regions (DMRs), gene enrichment, associations with blood gene expression (RNA-seq, n=119), and DNAm predictors of plasma proteins. Measurements and Main Results: Whole-blood DNAm at 73 CpGs and 550 DMRs was associated with 17 exacerbation-related microbiome traits (false discovery rate [FDR]ORMDL3 . Most CpGs were associated with Campylobacter (pharyngeal) and Leptotrichia (nasal) abundance. Ten DNAm markers were replicated ( p PTPRR associated with nasal bacterial richness. Enrichment analyses identified genes related to diabetes, obesity, smoking, TGF-β, MAPK, and Wnt signaling and regulated by trichostatin A, NF-κB, and the glucocorticoid receptor (FDRTannerella , was associated with ITM2C whole-blood expression. Nine DNAm-predicted plasma proteins involved in inflammation, tissue remodeling, and TGF-β signaling were associated with seven exacerbation-related microbiome traits, including Streptococcus and Selenomonas . Conclusions: Whole-blood DNAm markers implicated in inflammation, immunity, and asthma comorbidities were associated with the upper-airway microbiome linked to asthma exacerbations.

Background: Bronchodilator response (BDR) is a key clinical feature in childhood asthma, but its relation to asthma pathophysiology is not fully understood. This study examines the associations between BDR, disease control, and serum cytokines/chemokines in children with moderate‐to‐severe asthma (MSA). Methods: BDR was assessed in 140 children (aged 6–17 years, 41% females) from the SysPharmPediA cohort using the ERS/ATS 2022 guidelines (ΔFEV ₁ >10% predicted) and z ‐score (ΔFEV ₁ ‐ z ‐score >0.78) post‐bronchodilator definitions. Risk of uncontrolled asthma in relation to BDR was estimated by a logistic regression model, adjusting for baseline lung function, age, sex, BMI z ‐score, ethnicity, country, season, GINA step, and smoking exposure. Thirty‐nine serum proteins were measured using Luminex Multiplex Assay; levels below the detection limit (LOD) were imputed as LOD/√2, and proteins with >40% missing values across samples were excluded. Children with high and low BDR were compared for serum proteins by linear regression model, adjusting for covariates and applying false discovery rate correction. Results: Children with high BDR (21%) had significantly higher odds of uncontrolled asthma (adjusted OR ≈ 3.22, 95% CIs: 1.07–11.3) and more frequent severe exacerbations in the past year compared with those with low BDR (70% vs. 46%, p < .05). High‐BDR children showed elevated serum levels of IL‐13, IL‐4, TNF‐α, IL‐6, IL‐7, IL‐8, IL‐1β, and MMP‐1 ( q < 0.05). Conclusion: In children with MSA, a high BDR is independently associated with poorer asthma control and a distinct systemic inflammatory profile involving T2 and non‐T2 mediators. BDR may serve as a marker for asthma phenotyping. image

Background: The Respiratory Syncytial Virus (RSV) season of 2023/2024 was conspicuously different from previous seasons, with an abrupt decrease in hospitalisation rates at the peak of the season, leading to two lower peaks instead of the expected one high peak of hospitalisations. Thus, we investigated whether there was an interference with other virus infection waves in the course of that RSV season. Methods: We analysed RSV seasons since 2016 in children who were hospitalised due to an RSV infection in Eastern Bavaria and investigated epidemiological features of RSV seasons after the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic at local, regional, and national levels. Results: Analysing patterns of four RSV seasons prior to and three seasons after the SARS-CoV-2 pandemic, we found that the paediatric RSV hospitalisation wave of the 2023/2024 season was weaker and less pronounced than expected. When we compared detailed local, regional, and national surveillance data of other viral infections, we found that paediatric RSV hospitalisation waves were anticyclical to SARS-CoV-2 infection waves, but not to rhinovirus or influenza waves in the general population. Discussion: Our data suggests that concomitant SARS-CoV-2 infection waves in the general population may disrupt infection chains of RSV in children and, thus, decrease RSV-associated hospitalisation. This factor should be taken into account when assessing the effects of the upcoming RSV prophylaxis in the future.

Background: Early identification of children at risk of asthma attacks is important for optimizing treatment strategies. We aimed to integrate salivary microbiome and serum inflammatory mediator profiles with asthma attacks history to develop a comprehensive predictive model for future attacks. Methods: This study contained a discovery (SysPharmPediA) and a replication phase (U‐BIOPRED). School‐aged children with asthma were classified into at risk and no‐risk groups, based on the presence or absence of one or more severe attacks during one‐year follow‐up. Prediction models were developed using random forest on the training set (70%) with data on past asthma attacks, microbiome composition, serum inflammatory mediator levels, and their combinations and then tested on the rest of the population (30%). Outcomes were replicated in a subset of children with severe asthma from U‐BIOPRED. Results: Complete data were available for 154 children (SysPharmPediA = 121, U‐BIOPRED = 33). In discovery, the model based on past attacks resulted in an area under the receiving characteristic curve (AUROCC) ~ 0.7. Models including six salivary bacteria or six inflammatory mediators achieved similar results. The combined model incorporating seven features, past asthma attacks, Capnocytophaga , Corynebacterium , and Cardiobacterium , TIMP‐4, VEGF, and MIP‐3β achieved the highest accuracy with AUROCC ~0.87. The combined model in the U‐BIOPRED limited to available inflammatory mediators (VEGF), and incorporating past asthma attacks, Capnocytophaga, Corynebacterium, and Cardiobacterium , resulted in an AUROCC of 0.84. Conclusion: Serum inflammatory mediators and salivary microbiome complement asthma attacks history for predicting future attacks. These results highlight the imperative for continued investigation into oral microbiota and its interaction with the immune system.

Background: Asthma exacerbations (AEs) represent the major contributor to the global asthma burden. Although genetic and environmental factors have been associated with AEs, the role of epigenetics remains uncovered. Objective: This study aimed to identify whole blood DNA methylation (DNAm) markers associated with AEs in Europeans. Methods: DNAm was assessed in 406 blood samples from Spanish individuals using the Infinium MethylationEPIC microarray (Illumina). An epigenome‐wide association study was conducted to test the association of DNAm with AEs at differentially methylated positions, regions, and epigenetic modules. CpGs suggestively associated with AEs (false discovery rate [FDR] < 0.1) were followed up for replication in 222 European individuals, and the genome‐wide significance ( p < 9 × 10 ⁻⁸ ) was declared after meta‐analyzing the discovery and replication samples. Additional assessment was performed using nasal tissue DNAm data from 155 Spanish individuals. The effects of genetic variation on DNAm were assessed through cis‐methylation quantitative trait loci (meQTL) analysis. Enrichment analyses of previous EWAS signals were conducted. Results: Four CpGs were associated with AEs, and two were replicated and reached genomic significance in the meta‐analysis (annotated to ZBTB16 and BAIAP2 ). Of those, CpG cg25345365 ( ZBTB16 ) was cross‐tissue validated in nasal epithelium ( p = 0.003) and associated with five independent meQTLs (FDR < 0.05). Additionally, four differentially methylated regions and one module were significantly associated with AEs. Enrichment analyses revealed an overrepresentation of prior epigenetic associations with prenatal and environmental exposures, immune‐mediated diseases, and mortality. Conclusions: DNAm in whole blood and nasal samples may contribute to AEs in Europeans, capturing genetic and environmental risk factors.

Background/Objectives: Metered-dose inhalers (MDIs) and dry powder inhalers (DPIs) are common inhaled corticosteroid (ICS) inhaler devices. The difference in formulation and administration technique of these devices may influence oral cavity microbiota composition. We aimed to compare the saliva microbiome in children with moderate-to-severe asthma using ICS via MDIs versus DPIs. Methods: Saliva samples collected from 143 children (6–17 yrs) with moderate-to-severe asthma across four European countries (The Netherlands, Germany, Spain, and Slovenia) as part of the SysPharmPediA cohort were subjected to 16S rRNA sequencing. The microbiome was compared using global diversity (α and β) between two groups of participants based on inhaler devices (MDI (n = 77) and DPI (n = 65)), and differential abundance was compared using the Analysis of Compositions of Microbiomes with the Bias Correction (ANCOM-BC) method. Results: No significant difference was observed in α-diversity between the two groups. However, β-diversity analysis revealed significant differences between groups using both Bray–Curtis and weighted UniFrac methods (adjusted p-value = 0.015 and 0.044, respectively). Significant differential abundance between groups, with higher relative abundance in the MDI group compared to the DPI group, was detected at the family level [Carnobacteriaceae (adjusted p = 0.033)] and at the genus level [Granulicatella (adjusted p = 0.021) and Aggregatibacter (adjusted p = 0.011)]. Conclusions: Types of ICS devices are associated with different saliva microbiome compositions in moderate-to-severe pediatric asthma. The causal relation between inhaler types and changes in saliva microbiota composition needs to be further evaluated, as well as whether this leads to different potential adverse effects in terms of occurrence and level of severity.

Aim: Longevity accumulating in families has genetic and epigenetic components. To study early and unbiased epigenetic predictors of longevity prospectively, a birth cohort would be ideal. However, the original family longevity selection score (FLoSS) focuses on populations of elderly only. Methods: In the German birth cohort KUNO-Kids we assessed when information for such scores may be best collected and how to calculate an adapted FLoSS. Results: A total of 551 families contributed to adapted FLoSS, with a mean score of -0.15 (SD 2.33). Adapted FLoSS >= 7 as a marker of exceptional longevity occurred in 3.3% of families, comparable to original FLoSS in elderly. Conclusion: An adapted FLoSS from data collectable postnatally may be a feasible tool to study unbiased epigenetic predictors for longevity. TWEETABLE ABSTRACT In the German birth cohort KUNO-Kids we assessed if and how a family longevity selection score may best be calculated to study unbiased epigenetic predictors for longevity in the future.

Association of corticosteroid inhaler type with saliva microbiome in moderate-to-severe pediatric asthma Background Metered dose inhalers (MDIs) and dry powder inhalers (DPIs) are common inhaled corticosteroid (ICS) inhaler devices. The difference in formulation and administration technique of these devices may influence oral cavity microbiota composition. We aimed to compare the saliva microbiome in children with moderate-to-severe asthma using ICS via MDIs versus DPIs. Methods Saliva samples collected from 143 children (6-17 yrs) with moderate-to-severe asthma across four European countries (the Netherlands, Germany, Spain, and Slovenia) as part of the SysPharmPediA cohort were subjected to 16S rRNA sequencing. Microbiome was compared using global diversity (α and β) between two groups of participants based on inhaler devices (MDI (n=77) and DPI (n=65)) and differential abundance was compared using the Analysis of Compositions of Microbiomes with the Bias Correction (ANCOM-BC) method. Results No significant difference was observed in α-diversity between the two groups. However, β-diversity analysis revealed significant differences between groups using both Bray-Curtis and weighted UniFrac methods (Adjusted p-value=0.015 and 0.044, respectively). Significant differential abundance between groups, with higher relative abundance in the MDI group compared to the DPI group, was detected at the family level [Carnobacteriaceae (Adjusted p=0.033)] and at the genus level [ Granulicatella (Adjusted p=0.021) and Aggregatibacter (Adjusted p=0.011)]. Conclusion Types of ICS devices are associated with different saliva microbiome composition in moderate-to-severe pediatric asthma. The causal relation between inhaler types and changes in saliva microbiota composition needs to be further evaluated, as well as whether this leads to different potential adverse effects in terms of occurrence and level of severity.