HCA2.0 raw counts data, corresponding metadata, and TCR data

The second trimester of pregnancy is a critical period for fetal immune system development. Utilizing single-cell RNA sequencing (scRNA-seq) and T cell receptor sequencing (scTCR-seq) analyses, we construct a comprehensive immune cell atlas from 321 samples across 23 organs in second-trimester fetuses and adults. We identify a novel extrathymic CD4+ T subset that mediates the transition from TOX2+ precursor T cells to mature naive CD4 T cells. Our findings also reveal a widespread distribution of hematopoietic stem cells (HSCs) and memory/activated T cells in fetal organs, challenging the long-standing assumptions of fetal immune quiescence. Notably, clonal TCR sharing is observed among tissue-resident memory (TRM) T cells across various tissues, suggesting systemic immune involvement beyond local immunity at barrier sites. Furthermore, we uncover novel immune tolerance mechanisms, including the role of ARG1+ neutrophils and the PTGES3/PTGER4 signalling axis, which collectively suppress T cell activation in fetuses. Additionally, HSCs from non-canonical hematopoietic organs demonstrate the ability to differentiate into diverse immune lineages, highlighting alternative pathways for immune cell development. Collectively, these findings enhance our understanding of immune system maturation and tolerance during early human development, providing valuable insights into immune regulation in both fetal and adult contexts.