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Methylomic Analysis of Nasal Brushings Poorly Discriminates Subgroups in Pediatric Acute Respiratory Distress Syndrome

ABSTRACT: Pediatric acute respiratory distress syndrome (PARDS) is biologically heterogeneous. To determine whether the nasal epithelial methylome identifies subgroups of PARDS, we profiled genome-wide DNA methylation in nasal brushings from 21 children with PARDS and 3 pediatric ICU controls using the Infinium MethylationEPIC v2.0 array. After estimating and adjusting for cell-type composition, we performed unsupervised clustering and cell-type-specific differential methylation analysis. Cellular composition explained the majority of variation in the unadjusted methylome, and composition-adjusted clustering yielded only weak subgroup structure. These data indicate that, at this sample size, the nasal methylome poorly discriminates PARDS subgroups.

ORGANISM(S): Homo sapiens

PROVIDER: GSE337899 | GEO | 2026/07/07

REPOSITORIES: GEO

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Project description:Importance: Monocytes are plastic cells that assume different polarization states that can either promote inflammation or tissue repair and inflammation resolution. Polarized monocytes are partially defined by their transcriptional profiles that are influenced by environmental stimuli. The airway monocyte response in pediatric acute respiratory distress syndrome (PARDS) is undefined. Objectives: To identify differentially expressed genes and networks using a novel transcriptomic reporter assay with donor monocytes exposed to the airway fluid of intubated children with and at-risk for PARDS. To determine differences in gene expression at two time points using the donor monocyte assay exposed to airway fluid from intubated children with PARDS obtained 48-96 hours following initial tracheal aspirate sampling. Design, Setting and Participants: In vitro pilot study carried out using airway fluid supernatant from 57 children: 44 children with PARDS and 13 children at-risk for PARDS. Main Outcomes and Measures: We performed bulk RNA sequencing using a transcriptomic reporter assay of monocytes exposed to airway fluid from intubated children to discover gene networks differentiating PARDS from at-risk for PARDS. We also report differences in gene expression in children with PARDS 48-96 hours following initial tracheal aspirate sampling. Results: We found that interleukin (IL)-10, -4, and -13, cytokine/chemokine signaling, and the senescence-associated secretory phenotype are upregulated in monocytes exposed to airway fluid from intubated children with PARDS compared to those at-risk for PARDS. Signaling by NOTCH, histone deacetylation/acetylation, DNA methylation, chromatin modifications (B-WICH complex), and RNA polymerase I transcription and its associated regulatory apparatus were upregulation in children with PARDS 48-96 hours following initial tracheal aspirate sampling. Conclusions and Relevance: We identified gene networks important to the PARDS airway immune response using bulk RNA sequencing from a monocyte reporter assay that exposed monocytes to airway fluid from intubated children with and at-risk for PARDS. Mechanistic investigations are needed to validate our findings.

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Methylomic Analysis of Nasal Brushings Poorly Discriminates Subgroups in Pediatric Acute Respiratory Distress Syndrome

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