Integrative transcriptomic and proteomic profiling reveals altered thymocyte development and microenvironment remodeling during natural thymic atrophy.

Background: Age-related thymic atrophy (ARTA) is a hallmark of immunosenescence, yet the earliest thymocyte developmental checkpoints affected by increasing age and the coordinated molecular programs that drive thymic degeneration remain incompletely defined. Methods: We compared young (1-month-old) and middle-aged (MA, 12-month-old) male ICR mice using thymus weight/index measurement, histopathology, peripheral blood cell analysis, and immunostaining of thymic markers. We further performed RNA-seq and data-dependent acquisition (DDA) proteomics, followed by integrated transcriptomic-proteomic pathway analyses. Finally, we analyzed public human thymus datasets to assess the translational relevance of our findings. Results: Middle-aged mice exhibited marked thymic involution with reduced thymus weight and thymic index, accompanied by peripheral lymphopenia and reduced peripheral T-cell counts, while myeloid populations (neutrophils and monocytes) increased. Pathological examination revealed lipid droplet accumulation in the thymus of aged mice, along with decreased Ki-67 expression and an increased number of apoptotic cells. Histologically, aged thymuses showed cortical thinning and an indistinct corticomedullary boundary. Reduced cortical CD25 with increased CD44 is suggestive of a possible developmental impediment around the DN1-to-DN2 transition; in parallel, CD3 Conclusion: Increasing age disrupts early thymocyte differentiation and is accompanied by inflammatory-ECM remodeling and adipose-associated metabolic reprogramming. These integrative omics signatures nominate candidate pathways and regulators for developing interventions to mitigate ARTA and preserve immune homeostasis.