Pneumonia severity in sheep was more strongly associated with host regulation than with pathogen load. 2. IL1R2 was identified as a key hub gene underlying pneumonia resistance in sheep. 3. An enhancer variant at the IL1R2 locus was associated with reduced lung lesion severity. 4. Functional assays validated the regulatory role of IL1R2 in the epithelial response to Mycoplasma ovipneumoniae (M. ovipneumoniae) . Ovine pneumonia is a complex and economically devastating disease that results in approximately USD 4 billion in annual losses to the global livestock industry. Despite its substantial impact, the underlying pathogenic mechanisms and the host factors that confer resistance remain poorly understood. To address this knowledge gap, we employed an integrative multi-omics strategy to comprehensively investigate the genetic and microbial contributors to pneumonia resistance in sheep. To elucidate the pathogenic mechanisms underlying pneumonia resistance in sheep and to identify key host genetic and microbial determinants through the integration of multi-omics data with phenotypic information. We profiled the lung microbiome (metagenomics, n=61), host transcriptome (RNA-seq, n=61), and chromatin accessibility (ATAC-seq, n=14) in infected sheep. Whole-genome sequencing (WGS, n=61) data for the same animals were examined. Metagenomic profiling identified Jaagsiekte sheep retrovirus (JSRV) as the dominant pathogen across all samples, while disease severity was not driven by pathogen load. Transcriptomic analyses identified IL1R2 and CSF3 as key differentially expressed genes associated with resistance, with enrichment in cytokine-mediated immune pathways, including cytokine–cytokine receptor interaction and IL-17 signaling. ATAC-seq revealed globally increased chromatin accessibility in resistant sheep and significant enrichment of differentially accessible regions in immune-related pathways. Transcription factor footprinting revealed distinct regulatory landscapes, and high-resolution chromatin profiling identified dense binding of multiple transcription factors at the IL20RB promoter, including Hoxd12 and TF3A, indicating transcription factor–mediated regulation of IL20RB. Integrative multi-omics analysis identified IL1R2 as a central determinant of pneumonia resistance. IL1R2 expression was strongly correlated with chromatin accessibility at distal regulatory regions. A functional enhancer harboring the Single Nucleotide Polymorphism (SNP) chr3:99752986 exhibited increased accessibility and active histone marks in resistant sheep, and the protective A allele was significantly associated with reduced lung lesion severity. These findings were validated by Kompetitive Allele Specific PCR (KASP) genotyping and Quantitative real-time PCR (qRT-PCR). Functional assays further demonstrated that IL1R2 modulates host inflammatory responses. IL1R2 overexpression enhanced epithelial cell viability following Mycoplasma ovipneumoniae (M. ovipneumoniae) infection, whereas IL1R2 knockdown altered bacterial adhesion patterns, supporting its role in limiting excessive inflammatory signaling and maintaining epithelial integrity. This study emphasizes the importance of host-intrinsic factors in phenotypic variance in disease severity, identified key genetic and regulatory factors that could guide future therapeutic and breeding strategies.
Zhang et al. (Wed,) studied this question.