. Author manuscript; available in PMC: 2011 Dec 16.

Published in final edited form as: Nat Rev Immunol. 2011 Jul 22;11(8):544–549. doi: 10.1038/nri3028

Table 1.

Methods for studying RTE biology

Model system	Method	Advantages	Disadvantages	Refs
Intrathymic FITC injection	Labels developing thymocytes; FITC⁺ cells in the periphery are RTEs	Allows the phenotypic and functional analysis of the youngest RTEs by flow cytometry	Causes surgical stress Short time frame for FITC detection Labels mature T cells recirculating to the thymus	55,56
BrdU incorporation	BrdU is taken up by dividing thymocytes; RTEs are BrdU^low	A non-surgical procedure that allows the analysis of RTE phenotype	BrdU label is also taken up by dividing mature peripheral T cells Functional studies are precluded	57
TRECs	Quantification by PCR of excised DNA fragments generated during TCR rearrangement; RTEs are enriched for TRECs	Allows the determination of thymic output and the relative proportion of RTEs in the human T cell population	Precludes phenotypic and functional analysis Does not indicate time since thymic egress Cannot be used for analysis of single cells TREC⁺ cells may or may not be RTEs	58,59
Thymic lobe grafts	Congenic thymic lobes are grafted under the kidney capsule	Allows the phenotypic and functional analysis of RTEs by flow cytometry for up to 3 weeks	Creates an artificially full peripheral T cell compartment Causes surgical stress	18,60
Fetal thymus organ culture	Fetal thymic lobes are placed in culture; RTEs are harvested 1–12 days later	Allows the phenotypic and functional analysis of RTEs by flow cytometry	An in vitro system may not accurately reflect the in vivo environment	24
RAG2–GFP transgenic mice or RAG1–GFP knock-in mice	GFP signal remains detectable after RAG expression has ceased; GFP⁺ peripheral T cells are RTEs	Allows the phenotypic and functional analysis of RTEs from unmanipulated mice, and GFP signal intensity correlates with time since thymic egress	Division dilutes the GFP signal GFP signal is lower in CD8⁺ RTEs than in CD4⁺ RTEs	9,47,61
Cell surface phenotype	Mouse RTEs are QA2^lowCD24^hi	Allows for phenotypic and functional analysis of RTEs by flow cytometry	Excludes ~85% of RTEs	9
	Human RTEs are CD31⁺PTK7⁺		Markers are only expressed by CD4⁺ RTEs	3,62

BrdU, 5-bromodeoxyuridine; FITC, fluorescein isothiocyanate; GFP, green fluorescent protein; PTK7, protein tyrosine kinase 7; RAG, recombination-activating gene; RTE, recent thymic emigrant; TCR, T cell receptor; TREC, TCR, rearrangement excision circle.