Pneumonia infection perturbs the differentiation trajectory of thymic precursor T cells and contributes to neonatal thymic atrophy.

Objective This study aims to investigate the effects of pneumonia infection on T cell development in the infant thymus and its underlying mechanisms using histomorphology, RNA-seq technology, and flow cytometry.Methods Discarded thymus tissues were collected from 10 infants with congenital heart disease (aged 3–11 months) during cardiac surgery. Firstly, morphological changes of the thymus induced by pneumonia infection were assessed based on gross morphology and histomorphology. Subsequently, a flow cytometry analysis system was established based on specific surface markers of various subpopulations along the human thymic T‑cell developmental trajectory. This system was then used to analyze changes in the proportions of different cell subsets in the thymus of normal and pneumonia‑infected patients. Finally, early thymic progenitor cells from both normal and pneumonia‑infected patients were isolated by fluorescence‑activated cell sorting (FACS). RNA‑seq was performed to identify differentially expressed genes between the two groups. GO functional annotation and pathway enrichment analysis were established to explore the potential mechanisms through which pneumonia infection affects T‑cell development in the infant thymus.Results ① Histopathological and morphological analysis revealed that pneumonia infection led to atrophy of infant thymic tissue, with an increased proportion of cortical area and a decreased proportion of medullary area. Within the medullary area, the number of thymic corpuscles was significantly elevated, accompanied by a marked increase in their diameter. ② Flow cytometry analysis revealed that the proportion of early thymic progenitor cells (ETP-I) and single-positive CD4+ T cells in the thymus of patients with pneumonia infection significantly increased, while the proportion of late double-positive cells (LDP) significantly decreased. ③ RNA-seq revealed that pneumonia infection significantly altered gene expression in the CD45lo cell subpopulation within the infant thymus. Gene Ontology (GO) enrichment pathway analysis demonstrated that pneumonia infection notably upregulated pathways associated with T cell-mediated immunity, cell killing, apoptosome clearance, and B cell development, while downregulated pathways related to T cell migration, antigen processing and presentation, and T cell proliferation.Conclusion Pneumonia infection causes significant damages to the structure and function of the infant thymus. At the histological level, pneumonia infection leads to blurred corticomedullary demarcation and destruction of the thymic stroma, impairing the normal immunoregulatory microenvironment. At the functional level, pneumonia infection results in an abnormal upregulation in the proportion of early ETP-I and enhances their differentiation toward the B-cell lineage, which may be a key mechanism underlying the impaired T-cell development in the thymus due to pneumonia infection. This aberrant differentiation trend may further exacerbate thymic dysfunction and immune response imbalance in infants.