Transcriptomic landscapes of the endometrium of dairy cows with clinical or subclinical endometritis

Subclinical (SCE) and clinical endometritis (CE) are distinct manifestations of reproductive tract inflammatory disease in dairy cows. The development of both conditions stems from postpartum dysregulation of the inflammatory response or a shift in the composition of the uterine microbiome. To gain further insight into the host responses associated with these distinct conditions, we aimed to identify changes in the endometrial transcriptomic landscape in healthy postpartum dairy cows compared with those diagnosed with SCE or CE. Twenty-four multiparous Holstein cows were evaluated for uterine health status at 35 or 36 d postpartum using vaginal discharge scoring (Metricheck) and endometrial cytology (cytobrush). Based on these evaluations, cows were classified into 3 groups: healthy (n = 12; clear or no vaginal discharge and ≤5% endometrial PMN), SCE (n = 6; clear or no vaginal discharge and >5% PMN), and CE (n = 6; mucopurulent or worse discharge and >5% PMN). Endometrial samples collected via cytobrush were stored at -80°C and total RNA was isolated; RNA sequencing was performed using an Illumina NextSeq 500 platform, generating 75 bp single-end reads. Differentially expressed genes (DEG) were identified using DESeq2 with a significance threshold of P < 0.05 and |fold change| > 2. Pathway enrichment analyses were performed using the OmicShare platform to identify enriched biological pathways among the DEG. A total of 250 DEG were identified between healthy and SCE cows, 1,291 between healthy and CE cows, and 829 between SCE and CE cows. In SCE (as compared with healthy) cows, TNF, IL-17, NOD-like receptor signaling, and cytokine-cytokine receptor interaction pathways were upregulated, whereas the FoxO signaling pathway was downregulated. In CE compared with healthy cows, upregulated DEG were enriched in IL-17, TNF, chemokine, NOD-like receptor, NF-kappa B, and toll-like receptor signaling pathways, whereas downregulated DEG were enriched in PI3K-AKT, MAPK, AMPK, Wnt, PPAR, and metabolic pathways. In CE compared with SCE, upregulated DEG were enriched in NOD-like receptor, IL-17, chemokine, B cell receptor, and cytokine-cytokine receptor interaction pathways, and downregulated DEG were enriched in the metabolic pathways, fatty acid metabolism, insulin signaling pathway, and adipocytokine signaling pathway. These findings underscore that CE and SCE conditions involve an inflammatory event but likely arise from different mechanisms. The enrichment of immune signaling pathways in CE reflects a classic infectious response, whereas the metabolic and regulatory pathway alterations in SCE suggest a dysregulated inflammatory state linked to impaired resolution mechanisms. These results highlight the need for tailored prevention and treatment strategies, such as modulating immune regulation in SCE and targeting bacterial dysbiosis and tissue damage in CE cases.