ATS Congress 2026
Methylation Markers Related to Immunity and Asthma Comorbidities Are Associated with the Upper Airway Microbiome Linked to Asthma Exacerbations
Erick Castillo-Vargas, MSc1, Mario Martin-Almeida, MSc1, Elena Martin-Gonzalez, MSc1, Ruperto González-Pérez, MD, PhD2, José M. Hernández-Pérez, MD, PhD3,4, Olaia Sardón-Prado, MD, PhD5,6, Paloma Poza-Guedes, MD, PhD2, Elena Mederos-Luis, MD7, Paula Corcuera-Elosegui, MD, PhD5, Inmaculada Sánchez-Machín, MD, PhD7, Leyre López-Fernández, MD5, Jesús Villar, MD, PhD8,9,10,11, Andres Cardenas, PhD12, Fabian Lorenzo-Diaz, PhD1, Maria Pino-Yanes, PhD1,8,13, Javier Perez-Garcia, PhD1,12
1 Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain.
2 Severe Asthma Unit, Allergy Department, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain.
3 Pulmonary Medicine Service, Hospital Universitario de N.S de Candelaria, La Laguna, Tenerife, Spain.
4 Pulmonary Medicine Section, Hospital Universitario de La Palma, La Palma, Spain.
5 Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain.
6 Department of Pediatrics, University of the Basque Country (UPV/EHU), San Sebastián, Spain.
7 Allergy Department, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain.
8 CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
9 Multidisciplinary Organ Dysfunction Evaluation Research Network (MODERN), Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain.
10 Faculty of Health Sciences, Universidad del Atlántico Medio, Tafira Baja, Las Palmas, Spain.
11 Li Ka Shing Knowledge Institute at the St. Michael’s Hospital, Toronto, Ontario, Canada.
12 Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, USA.
13 Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain.
Rationale: The upper airway bacterial taxa and diversity indices associated with asthma exacerbations are partially regulated by host genetic variants implicated in immunity and asthma comorbidities as revealed by genome-wide approaches. However, the contribution of epigenetic modifications such as DNA methylation (DNAm) remains unexplored. Thus, we aimed to identify leukocyte epigenetic markers associated with the upper airway microbiome linked to asthma exacerbations.
Methods: We analyzed nasal, pharyngeal, saliva, and blood samples from 197 adults and 52 children from the GEMAS study. Leukocyte DNAm was profiled using the Illumina MethylationEPICv1 array and the salivary, nasal, and pharyngeal microbiome by targeted sequencing of the 16S-rRNA gene (V3-V4 regions). We performed microbiome epigenome-wide association studies (mbEWAS), testing 731,223 CpG sites for associations with three alpha-diversity indices (Observed, Shannon, and Faith) and 18 bacterial genera previously associated with asthma exacerbations. Linear regression models were adjusted for age, sex, ancestry, and cell-type heterogeneity. We meta-analyzed age groups and tested differentially methylated regions (DMRs). Multiple comparisons were adjusted using a false discovery rate (FDR)<0.05. We examined whether suggestively associated DNAm markers (p<5x10-5) participate in any biological pathway or trait through enrichment analyses using EWASToolskit and Enrichr.
Results: DNAm levels at 59 CpG sites were associated with the abundance of Fusobacterium, Leptotrichia, Porphyromonas, Streptococcus, Campylobacter, Bifidobacterium, Capnocytophaga, and α-diversity indices. Two CpGs mapped to FOXA2 and THBS1, both previously described as potential therapeutic targets for asthma. Enrichment analysis revealed an overrepresentation of CpGs related to asthma, atopy, air pollution, and smoking (p<1x10-3). Additionally, we detected 239 DMRs linked to the exacerbation-related bacterial genera and 162 DMRs associated with the alpha-diversity indices. Notably, four DMRs were in genes implicated in asthma pathogenesis (CHIT1, ADAMTS9, CDH26, and ALCAM). Gene-set enrichment analysis of CpGs and DMRs showed an overrepresentation of genes involved in asthma-related pathways (Wnt, IL-2, IL-3, IL-6, mTOR, and TGF-β signaling) and comorbidities (atopy, smoking, and obesity). Additionally, we observed an enrichment in genes interacting with trichostatin A, a potential drug for asthma exacerbations.
Conclusions: Our study revealed novel associations of leukocyte DNAm with the composition of the upper airway microbiome involved in asthma exacerbations. These methylation patterns are linked to immune and inflammatory pathways, asthma comorbidities, and putative drug targets for asthma exacerbations. These results support that host-microbiome interactions may influence asthma exacerbations through epigenetics.
Funding: MICIU/AEI/10.13039/501100011033 (PID2020-116274RB-I00), Fundación DISA (009/2024), Catalina Ruiz Program (ACIISI), FPU(FPU24/00854).
Doi: https://doi.org/10.1093/ajrccm/aamag162.531