Epigenetic patient stratification reveals a sub-endotype of type 2 asthma with altered B-cell response

Despite biomarker-guided treatment strategies, clinical outcomes among patients with type 2 (T2)-high asthma remain heterogeneous, with some patients responding poorly to T2-targeted biologic therapies. We developed a contrastive machine learning method for patient stratification based on whole-blood DNA methylation (DNAm), applying it to pediatric asthma cohorts of Latino (discovery; n=1,016) and African American (replication; n=429) children. The resulting DNAm stratification score revealed a continuum of clinical severity and drug response within the T2-high asthma endotype. Molecular profiling of high-score asthma patients identified eosinophil-specific hypermethylation—validated in an independent Canadian adult cohort using purified eosinophil DNAm—as well as upregulation of canonical T2-associated genes. Transcriptomic analysis of elevated DNAm scores within T2-high patients further uncovered a gene signature linked to B-cell lineage activity, predominantly reflecting plasma cell activity orthogonal to canonical T2 inflammation programs. This defines a previously unrecognized sub-endotype, which we term T2-high asthma with Altered B Cell response (T2ABC). In a randomized controlled trial of the anti-IgE biologic omalizumab in primarily White adult T2-high asthmatic patients (n=300), the T2ABC gene expression signature was prognostic of poor outcomes, including a 24% mean increase in disease exacerbation rates compared to the trial baseline (P=0.004), which could not be explained by treatment or placebo assignment. Patients treated with omalizumab showed better outcomes than patients in the placebo arm within the T2ABC-low group (P=0.019) but not within the T2ABC-high group (P=0.48), suggesting that IgE blockade does not adequately target the pathogenic mechanisms active in T2ABC-high disease. Single-cell transcriptomic analysis demonstrated that the T2ABC signature reflects heightened activity of non-IgE plasma cells, consistent with the presence of additional antibody isotype responses in a form of severe asthma arising within a T2-high immunologic context. Our findings, replicated and validated across four ancestrally and ethnically diverse pediatric and adult cohorts, support the use of DNAm- and transcriptome-based patient stratification to refine drug development, eligibility, and administration strategies for improving precision in T2 asthma therapy.