Analysis of Human Thymopoiesis Reveals Rapid Postnatal Remodeling of Thymocytes Within the First 3 Months of Life

ABSTRACT

The thymus generates a diverse and self‐tolerant T‐cell repertoire. Its development and output undergo profound changes from fetal to early postnatal life, yet the dynamics of this transition remain incompletely understood. Here, we performed a comprehensive analysis of human thymopoiesis across the perinatal (birth to <10 days), early postnatal (10 days–3 months), and homeostasis (>3 months) periods using high‐dimensional flow cytometry and signal joint T‐cell receptor excision circle (sjTREC) quantification. Within the perinatal phase, the thymus exhibits the highest intrathymic production, with elevated frequencies of CD4 ⁺ T cells and unconventional T cell (UTC), including regulatory T cells (Tregs). After 10 days of age, the frequency of double‐positive (DP) thymocytes increases and is associated with dynamic thymocyte phenotypic shifts that suggest enhanced progenitor commitment and proliferation, accompanied by reduced T‐cell receptor (TCR) signaling strength. Early postnatal UTCs (birth to 3 months) display a distinct phenotype compared with those generated after 3 months. We notably identified a postnatal wave of effector Vδ2 ⁺ γδ T cells emerging between 10 days and 3 months of age. These findings suggest a transition in human thymopoiesis from an early effector‐prone unconventional output to predominantly conventional T‐cell production after 3 months, highlighting a critical window in immune system establishment.