maintenance, cell death and compromised organ function. This is first observed in the thymus, the
primary lymphoid organ that generates and selects T cells. However, the molecular and cellular
mechanisms underpinning these ageing processes remain unclear. Here, we show that mouse
ageing leads to less efficient T cell selection, decreased self-antigen representation and increased T
cell receptor repertoire diversity. Using a combination of single-cell RNA-seq and lineage-tracing,
we find that progenitor cells are the principal targets of ageing, whereas the function of individual
mature thymic epithelial cells is compromised only modestly. Specifically, an early-life precursor cell
population, retained in the mouse cortex postnatally, is virtually extinguished at puberty.
Concomitantly, a medullary precursor cell quiesces, thereby impairing maintenance of the
medullary epithelium. Thus, ageing disrupts thymic progenitor differentiation and impairs the core
immunological functions of the thymus.
Bibliographical noteAcknowledgements: We gratefully acknowledge the Chan Zuckerberg Biohub for support and for sequencing, and mem-
bers of the Tabula Muris Consortium for technical assistance. CPP is funded by the MRC
(MC_UU_00007/15). CPP, GH, JB and MDM were supported by the Wellcome Trust (grant 105045/
Z/14/Z). JCM was supported by core funding from the European Molecular Biology Laboratory and
from Cancer Research UK (award number 17197). GH and ICA was supported by the Swiss National
Science Foundation (grant numbers IZLJZ3_171050 and 310030_184672). AEH was supported by a
Clinical Lectureship from the NIHR. FD was supported by the Wellcome Trust [109032/Z/15/Z].
Data Availability StatementAll code used to process data and perform analyses is available from https://github.com/WTSA-
Homunculus/Ageing2019 (Baran-Gale, 2020; copy archived at https://github.com/elifesciences-pub-
lications/Ageing2019). All sequence data, counts matrices and meta-data are available from ArrayEx-
press with accession numbers E-MTAB-8560 (ageing thymus) and E-MTAB-8737 (lineage traced
thymus). TCR sequencing data is available from SRA (PRJNA551022).