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The full spectrum of human

naive T cells
Theo van den Broek1,2,3, José A. M. Borghans1 and Femke van Wijk1*
Abstract | Naive T cells have long been regarded as a developmentally synchronized and fairly
homogeneous and quiescent cell population, the size of which depends on age, thymic output
and prior infections. However, there is increasing evidence that naive T cells are heterogeneous in
phenotype, function, dynamics and differentiation status. Current strategies to identify naive
T cells should be adjusted to take this heterogeneity into account. Here, we provide an integrated,
revised view of the naive T cell compartment and discuss its implications for healthy ageing,
neonatal immunity and T cell reconstitution following haematopoietic stem cell transplantation.

Lymphopenia The naive T cell pool is generally considered to be a fairly What defines a naive T cell?
The condition of having an quiescent, homogeneous pool of antigen-​inexperienced After being subjected to positive and negative selec-
abnormally low level of cells. However, recent studies have revealed important tion in the thymus, T cells migrate to the periphery and
lymphocytes in the circulation. differences between naive T cells in terms of phenotype, enter the naive T cell compartment. In the periphery,
Haematopoietic stem cell
dynamics, differentiation status, location and function. naive T cells continuously recirculate between sec-
transplantation This heterogeneity may be influenced by factors such as ondary lymphoid organs and blood via the lymphatic
(HSCT). Treatment of recipients age, thymic function and total numbers of T cells and system by expressing the lymphoid homing receptors
with irradiation and/or tends to be overlooked in most immunological studies, CC-​chemokine receptor 7 (CCR7) and CD62 ligand
chemotherapy followed by the
even though it affects the performance of the immune (CD62L; also known as L-​selectin) (Table 1). In response
infusion of cells containing
haematopoietic stem and
system. These insights call for a revised view of the naive to encountering and interacting with cognate antigens
progenitor cells with or without T cell pool. in the periphery, naive T cells will proliferate and dif-
immune cells derived from Although mouse studies have substantially con- ferentiate into different types of effector and memory
individuals of the same species. tributed to our understanding of the human T cell T cells, which can migrate to different tissues for local
compartment, the generation, maintenance and func- antigen patrol. To ensure adequate immune responses
tion of the naive T cell pool greatly differs between against newly encountered pathogens, the naive T cell
mice and men1–3. These differences impose obvious compartment must maintain a large number of cells
limitations for the extrapolation of insights obtained with unique T cell receptors (TCRs) in a limited phys-
from mice to humans when trying to understand ical space. This requirement is challenging, because
naive T cell biology, including naive T cell reconsti- in both humans and mice, the thymus involutes and
tution after  lymphopenia, the effects of ageing on the atrophies with age; homeostatic proliferation and sur-
naive T cell compartment and factors important for vival of T cells are thought to compensate for this loss
Laboratory of Translational T cell maintenance. but can lead to the outgrowth of certain T cell clones at
Immunology, University
In this Review, we focus on data obtained from the expense of others. Strong indications exist that this
Medical Centre Utrecht,
Utrecht, Netherlands. humans and review recent findings that expose the challenge is overcome differently in mice and humans.
Department of Medical
varying levels of heterogeneity in the naive T cell In mice, throughout life, peripheral T cell proliferation
Microbiology, University compartment. On the basis of three examples, we hardly contributes to the maintenance of the naive T cell
Medical Centre Utrecht, discuss the implications of these insights for health pool. By contrast, the maintenance of the naive
Utrecht, Netherlands. and disease. We discuss how reduced immune T cell pool in human adults is almost entirely depend-
Program in Cellular and responses to infection and vaccination in elderly ent on peripheral T cell proliferation1,2. Furthermore,
Molecular Medicine, Boston
individuals are related to changes in their naive naive T cells in humans are extremely long-​lived, with
Children’s Hospital and
Department of Pediatrics,
T cell pool. Following this, we cover how similarly expected lifespans of 6–9 years, in contrast to those
Harvard Medical School, reduced immune responses in neonates are related in mice, which are replaced every 6–11 weeks1,2. The
Boston, MA, USA. to completely different characteristics of their naive survival and proliferation of naive T cells is promoted
*e-​mail: T cell pool. Finally, we argue that immune recovery by homeostatic factors, such as IL-7 and self-​peptide after  haematopoietic stem cell transplantation (HSCT) MHC complexes4. Under steady-​state conditions, these needs to be monitored more closely, owing to the factors lead to naive T cell pool turnover and mainte-
s41577-018-0001-y slow reconstitution of the naive T cell compartment. nance, and do not lead to accelerated differentiation of

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Homeostatic proliferation
naive T cells towards effector or memory T cell subsets. RTE is confusing because ‘recent’ mostly refers to the
This term can refer to two However, under lymphopenic conditions, the same cues immaturity of the naive T cell in terms of lack of prior
different phenomena: the are thought to induce accelerated differentiation4. This proliferation and developmental steps and may not be
steady-​state maintenance of example illustrates that homeostatic proliferation may related to the actual age of the cell. Thus, RTEs also form
T cells through self-​renewal
(minimal division) and the
have different outcomes in different settings. However, it a heterogeneous population of cells with respect to the
process by which T cells in remains unclear to what extent this proliferation affects point in time at which they were released by the thymus.
lymphopenic conditions the function and dynamic properties of naive T cells. Measuring the contribution of RTEs to the naive T cell
rapidly proliferate to Functionally, T  cells are considered naive until pool is not straightforward. A commonly used method
reconstitute the T cell pool,
they encounter their cognate antigen in the periphery is the measurement of  T  cell receptor excision circles
also called lymphopenia-​
induced proliferation.
and differentiate into effector or memory T cells. As (TRECs)1,10–14. Cell division leads to a decline in the
it is difficult to assess a prior history of antigen recog- average number of TRECs per T cell, because TRECs
Virtual memory T cells nition of T cells in vivo, surface marker expression is are not copied during cell division and are randomly dis-
Antigen-​inexperienced commonly used to identify naive T cells. In humans, tributed among daughter cells14–16. Thus, TRECs do not
memory-​phenotype T cells,
which may be induced by T cell
naive T cells express CD45RA and lack expression of directly reflect thymus output, and TREC-​based analyses
receptor cross reactivity, low-​ the memory-​associated marker CD45RO (Table  1). of RTEs may be confounded by the presence of TRECs
affinity peptide and/or MHC Expression of at least one extra naive T cell marker (for in T cells that have already undergone T cell division.
ligands and certain cytokines. example, CCR7, CD62L or CD27 (Table 1)) is required Another disadvantage of using TRECs for the identifi-
to distinguish naive T cells from terminally differen- cation of RTEs is that cells cannot be sorted on the basis
Mature naive T cells
Naive T cells that have matured
tiated effector memory T (TEM) cells, which lack the of their TREC content, impeding their further analysis.
in secondary lymphoid organs expression of CCR7, CD62L or CD27 markers but re-​ Surface expression of the immunoreceptor tyrosine-​
following thymic egress and are express CD45RA (CD45RA+ TEM cells)5. Although dif- based inhibitory motif receptor CD31 (also known as
no longer recent thymic ferent laboratories have their own ‘favourite’ naive T cell PECAM1; Table 1) on naive CD4+ T cells can identify a
markers, most of these actually select for highly over- T cell population that is enriched in RTEs8,17–20. CD31+
T cell receptor excision lapping pools of naive T cells. Therefore, in steady-​state naive T cells contain higher TREC levels — suggesting
circles conditions, a CD45RA+CD45RO– state in combination that they have undergone fewer rounds of division —
(TRECs). Small, stable circles of with CCR7, CD62L or CD27 expression is sufficient to than CD31– naive T cells, they have a more diverse TCR
DNA excised during T cell
cover the vast majority of naive T cells while excluding repertoire9 and the percentage of CD31+ naive T cells
receptor gene rearrangement
in the thymus.
CD45RA+ TEM cells. However, it is important to realize declines with age1,18 and after neonatal thymectomy21;
that this naive T cell identification system will include all of these points suggest the usefulness of CD31 as a
small populations of functionally distinct T cell subsets, potential marker for RTEs. However, there are a few
such as forkhead box protein P3 (FOXP3)-expressing limitations of the use of CD31. Following TCR stimu-
regulatory CD4+ T (Treg) cells, stem cell memory T lation, CD31 expression is downregulated by enzymatic
(Tscm) cells and memory T cells with a naive phenotype shedding22, but it may be re-​expressed under specific
(BOX 1). Conversely, memory-​phenotype T cells that may conditions such as lymphopenia22. For CD8+ RTEs, the
be antigen-​inexperienced, such as virtual memory T cells association with increased CD31 expression is less clear
and innate memory T cells, are excluded6. A system that because CD8+ T cells ubiquitously express this marker23.
distinguishes naive T cells on the basis of the lack of Instead, CD103 (also known as integrin αE) has been
expression of transcription factors associated with dif- proposed to identify CD8+ RTEs, as CD8+CD103+
ferentiation, as discussed below, could be valuable for a naive T cells have a fairly high average TREC content
stricter definition of naive T cells. It is beyond the scopeand show a clear age-​associated and thymectomy-​
of this Review to elaborate on all T cell subtypes; how- associated decline24. In addition, expression of CD31
on naive CD4+ T cells does not imply that these cells
ever, this illustrates that what is defined as a ‘naive’ T cell
strongly depends on the exact definition and context have never divided. The average TREC content of CD31+
and that, in fact, the naive effector and memory T cell naive T cells declines with age, which demonstrates
compartments are not so strictly separated. that they renew by proliferation, possibly driven by
cytokine-​induced homeostatic proliferation19.
The naive T cell spectrum Recent findings indeed indicate that there is also
It has recently become clear that the naive T cell defi- heterogeneity within the CD31+ naive T cell population
nition covers a whole spectrum of cells with different (Fig. 1). Expression of protein-​tyrosine kinase 7 (PTK7)
properties (Fig. 1); it is important to appreciate these is associated with CD4+ RTEs8 but, in contrast to CD31,
differences because they may play an important role in is downregulated in vitro upon cytokine-​induced pro-
clinical settings. liferation without TCR stimulation8,21. The production
of CXC-​chemokine ligand 8 (CXCL8; also known as
Recent thymic emigrants: the youngest naive T cells. IL-8) by CD4+ or CD8+ naive T cells shows a similar
Naive T  cells that have recently egressed from the pattern21,25. RTEs have long been known to lack or pro-
thymus are commonly described as recent thymic duce only low levels of hallmark effector cytokines such
emigrants (RTEs)7. RTEs are functionally different as IFNγ and IL-4 (REFS.  19,25). Gibbons and colleagues
from mature naive T cells (Fig. 1) as RTEs show reduced were the first to demonstrate that human (and not
proliferation and cytokine production upon stimula- mouse) naive CD4+ and CD8+ T cells have the unique
tion8. As the thymus is the only origin of T cells with new feature of producing IL-8 (REF.  3). IL-8 production is
specificities, the RTE population is also the most TCR-​ highly enriched in the CD31+PTK7+ fraction and is lost
diverse part of the naive T cell pool9. In itself, the term within CD31+ cells following in vitro cytokine-​induced
© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Table 1 | Surface markers associated with a T cell naive phenotype

marker Ligands Expression Function Refs
CD45RA and Unknown CD45RO is preferentially expressed on memory CD45 phosphatase activity plays a role 113–116

CD45RO (isoforms T cells in TCR signal transduction, and the SFKs

of the leukocyte have been identified as its primary targets
common antigen) CD45RA is expressed on naive T cells and
effector memory T cells
CD45RO and CD45RA dual expression occurs
when naive T cells differentiate into effector or
memory T cells and when TEM cells re-​express
As such, exclusion of CD45RO-​expressing
cells within the CD45RA+ T cell pool is
recommended when identifying naive T cell
CCR7 CCL19 and CCL21 CCR7 is expressed at high levels on CD4+ and CCR7 is involved in the homing of T cells 5,117

CD8+ naive T cells and TCM cells but not on to various secondary lymphoid organs by
TEM cells and CD45RA+ TEM cells mediating extravasation via HEVs
CCR7 and CD45RA co-​expression is used to
distinguish naive T cells from CD45RA+ TEM cells
This is of particular importance for CD8+ T cells,
which show a relatively high proportion of
CD45RA+ TEM cells compared with CD4+ T cells
CD62L GLYCAM1, CD34 CD62L is expressed at high levels on CD4+ and CD62L is a cell adhesion molecule 115,118–120

and MADCAM1 CD8+ naive and TCM cells, but TEM cells show involved in homing of T cells to various
heterogeneous expression secondary lymphoid organs
CD62L and CD45RA co-​expression is used to Through rolling adhesion, CD62L
distinguish naive T cells from CD45RA+ TEM cells decelerates lymphocytes by engaging
ligands expressed on HEVs
This is of particular importance for CD8+ T cells,
which show a relatively high proportion of
CD45RA+ TEM cells compared with CD4+ T cells
CD31 CD38, CD31, CD31 is expressed on naive CD4+ T cells that CD31 has been shown to inhibit TCR 18,19,107 ,121

integrin αvβ3 and have recently egressed from the thymus signalling in T cells through the action
glycosaminoglycans (for example, RTEs) of protein-​tyrosine phosphatases (SHIP,
SHP1 and SHP2), which are recruited
CD31 may be (re-) expressed on memory CD4+ by its immunoreceptor tyrosine-​based
T cells under specific conditions inhibition motif
CD31 is abundantly expressed by CD8+ naive
T cells; therefore, CD31 expression does not
uniquely identify CD8+ RTEs
CD27 (member CD70 CD27 is expressed by almost all CD4+ and CD8+ CD27 plays an important role in T cell and 108,122–128

of the TNFR naive T cells T cell–B cell interactions and provides

superfamily) co-​stimulatory signals required for the
generation and long-​term maintenance
of T cell immunity
CD27 expression can also be found on CD27− T cells arise after long-​term
CD45RA+CD8+ TEM cells and, in conjunction antigenic stimulation and indicate a late
with CD28, is used to identify different stage of differentiation
CD45RA+ TEM subsets
CD28 CD80 and CD86 CD28 is expressed by all naive T cells; however, CD28 provides co-​stimulatory signals 108,126,129–134

expression is not limited to naive T cells required for T cell activation and survival;
TCR activation without CD28 co-​
stimulation results in T cell anergy
CD28 expression decreases with age, The lack of CD28 expression on CD8+
predominantly for CD8+ T cells T cells, and to a lesser extent on CD4+
T cells, is associated with terminal
CD28 expression can be found on The CD8+CD28− fraction is expanded
CD45RA+CD8+ TEM cells and, in conjunction in elderly individuals as well as in
with CD27, is used to identify different chronic viral infection, malignancies and
CD45RA+ TEM subsets autoimmunity
CCL , CC-​chemokine ligand; CCR , CC-​chemokine receptor ; CD62L , CD62 ligand; GLYCAM1, putative glycosylation-​depended cell adhesion molecule 1;
HEVs, high endothelial venules; MADCAM1, mucosal addressin cell adhesion molecule 1; RTEs, recent thymic emigrants; SFKs, Src family of protein tyrosine
kinases; SHIP, phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1; SHP1, tyrosine-​protein phosphatase non-​receptor type 6; SHP2, tyrosine-​protein
phosphatase non-​receptor type 11; TCM cell, central memory T cell; TCR , T cell receptor ; TEM cell, effector memory T cell; TNFR , tumour necrosis factor receptor .

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Box 1 | Naive-​like T cells

Regulatory T cells
regulatory CD4+ t (treg) cells represent a specific lineage that plays a crucial role in the maintenance of self-​tolerance and
immune homeostasis88,89. although treg cells can be induced in the periphery, the majority of circulating Treg cells are
generated in the thymus. T cells are thought to adopt a Treg programme in the thymus when they have a higher T cell
receptor (tCr) affinity for a self-​peptide than non-​treg CD4+ T cells90,91, and treg differentiation is further dependent on
both IL-2 and IL-15 (REF. 92). treg cells that exit the thymus express classical naive T cell markers, including CD45RA,
CC-​chemokine receptor 7 (CCR7) and CD62 ligand (CD62L), but, in contrast to conventional naive T cells, express
relatively low levels of IL-7 receptor-​α (CD127). When assessing the conventional naive CD4+ T cell compartment,
treg cells can be excluded based on forkhead box protein P3 (FOXP3) and/or CD25 expression in combination with low
CD127 expression93.
Stem cell memory T cells
Within the CD45RA+CCR7+CD4+ or CD8+ T cell compartments, a proportion of T cells are distinct from truly naive T cells
as they show phenotypical and functional characteristics reminiscent of effector and memory T cells. Among these
naive-​like memory T cells, a subset termed stem cell memory T (Tscm) cells is characterized by the expression of CD95,
CD122, CXC-​chemokine receptor 3 (CXCR3) and the integrin CD11a (β2 integrin subunit of LFA1)94–97. These cells express
a substantially lower T cell receptor excision circle (TREC) content than the naive T cell population as a whole, similar to
non-​naive T cells, and can rapidly acquire effector functions upon antigenic and homeostatic stimulation. Despite low
TREC levels, high expression levels of the intracellular proliferation marker Ki-67 and a restricted TCR repertoire98
(all characteristics that suggest that they have undergone several rounds of division), tscm cells maintain their naive-​like
phenotype. These cells have stem-​cell-like properties of self-​renewal, can persist for decades94–97 and are maintained by
extensive proliferation97 (Fig. 1).
Memory T cells with a naive phenotype
Another naive-​like memory subset of CD8+ T cells was recently identified that shows high expression of CXCR3 and
CD49d, high IFNγ production and high T-​box transcription factor TBX21 expression but that phenotypically and
transcriptionally differed from characteristic memory and effector T cells99. Although naive-​like memory T cells show
similar telomere lengths to naive T cells, CD8+ naive-​like memory T cells have a restricted TCR Vβ repertoire, suggesting
that these cells underwent antigen-​driven expansion99. RNA sequencing analysis placed CD8+ naive-​like memory T cells
in between naive and central memory T cells, similar to Tscm cells99. Whereas CXCR3 expression is similar for these two
naive-​like memory T cell populations, naive-​like memory T cells and Tscm cells differ phenotypically in terms of CD95,
CD122 and CD11a expression99. Although naive-​like memory T cells phenotypically appear as naive T cells, the current
view is that because they are antigen-​experienced they should be considered as the least differentiated stage of the
memory T cell pool and not be incorporated within the naive T cell compartment.

proliferation and following neonatal thymectomy21. Although the signals that drive RTE maturation are
Interestingly, although IL-8 expression is imprinted early largely unknown, the route of T cell differentiation may be
during thymic selection, IL-8 expression is relatively metabolically and epigenetically regulated30–32. Epigenetic
low in mature single-​positive thymocytes in contrast to mechanisms — including DNA methylation, histone mod-
PTK7 expression, which is already high in mature single-​ ifications and non-​coding RNAs — regulate rearrange-
positive thymocytes21,25. It remains to be elucidated ment of chromatin to promote or prevent gene expression.
whether IL-8 production is induced extrathymically or The chromatin accessibility landscape has been shown
whether naive T cells that are about to egress from the to differ greatly between naive and memory T cells33,34.
thymus upregulate IL-8. Recently, it was shown that Human naive CD8+ T cells were found to have increased
the most immature RTE fraction is also enriched for accessibility and expression of transcription factors related
complement receptor type 1 (CR1) and CR2 expres- to, for example, TCR signalling, whereas memory CD8+
sion26. Together, PTK7, IL-8, CR1 and CR2 seem to T cells exhibit greater accessibility and expression of tran-
identify the least-​differentiated RTEs. scription factors related to T cell differentiation and effec-
tor function34. For human CD4+ T cell differentiation, a
Naive T cell maturation and differentiation. RTEs progressive loss of DNA methylation from naive T cells to
are thought to undergo maturation in secondary lym- central memory T (TCM), TEM and CD45RA+ TEM cells has
phoid organs before they gain full functional compe- been observed. In addition, FOXP1 has been proposed
tency. Mature naive T cells show higher proliferation, as a candidate gatekeeper transcription factor of CD4+
cytokine production and expression of early activation T cell ‘naivety’33. Although these data clearly show that
markers (including CD25) upon antigen encounter naive T cells have reduced expression and accessibility of
than RTEs27. In humans, CD25dim naive T cells show transcription factors that are associated with differentia-
signs of prior activation, as they have lower expression tion compared with memory T cells33,34, little is known as
of CD45RA and higher expression of the intracellular yet about differences within the naive T cell compartment.
proliferation marker Ki-67 than CD25− naive T cells. Recent studies in mice, which show that RTEs and mature
Although their TREC content is lower than that of naive T cells exhibit differential DNA methylation levels
CD25− naive T cells, CD25dim naive T cells still show a at key cytokine (Il2 and Il4) loci, suggest that epigenetic
broad TCR Vβ repertoire28,29, which suggests that they regulation also acts as a mechanistic basis for post-​thymic
are not very far along the T cell differentiation pathway. naive T cell maturation30.
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Cytokines TCR

Thymus RTE CD31+ CD31– Tscmcells Effector T cells

memory T cells
Mature naive T cells
Marker T cell subset
TREC CD4+, CD8+ ++ + +/– –
PTK7 CD4+ + – – –
CD31 CD4+ + + – –
CD103 CD8+ + – – –
IL-8 CD4+, CD8+ + +/– +/– –
CR2 CD4+, CD8+ + +/– +/– –
CD25 dim
CD4+ – +/– +/– –
CD95 (FAS) CD4+, CD8+ – – – ++
CD122 (IL-2Rβ) CD4+, CD8+ – – – ++

TCR diversity


Proliferation +/– + + +++ ++

Fig. 1 | Schematic representation of naive T cell differentiation. After their egress from the thymus, CD4+ recent thymic
emigrants (RTEs) express high levels of protein-​tyrosine kinase 7 (PTK7) and CD31, whereas CD8+ RTEs express CD103.
Both CD4+ and CD8+ RTEs express complement receptor 2 (CR2) and produce IL-8 (REFS. 8,17–21,26). Cytokine stimulation of
RTEs results in the loss of PTK7 expression and lower production of IL-8 but maintenance of CD31 expression8,21.
Subsequent T cell receptor (TCR) signalling, which is triggered upon the naive T cell encountering its cognate antigen,
results in skewing towards a CD31− naive T cell phenotype and possibly effector and memory T cell differentiation,
depending on the strength of the TCR trigger. Although the figure does not depict this possibility , we cannot exclude that
cells in the different naive T cell subsets may differentiate more directly towards an effector or memory phenotype without
going through all the depicted differentiation steps. RTE and naive T cell differentiation are thought to occur outside of the
circulation in secondary lymphoid organs or tissue. The expression of CD25dim on CD31+ and CD31− naive CD4+ T cells
suggests activation and proliferation with corresponding lower T cell receptor excision circle (TREC) content28,29. It is
thought that CD31− and CD31+ naive T cells can directly differentiate towards effector T cells or differentiate towards
stem cell memory T (Tscm) cells. Tscm cells have stem-​cell-like properties of self-​renewal and express typical naive T cell
markers but additionally express markers such as CD95 and CD122 characteristic of effector T cell differentiation94–97.
Human naive T cells can self-​renew via low-​affinity TCR triggering and/or cytokine stimulation, but their proliferation rates
are lower than those of Tscm cells and effector and memory T cells97. TCR diversity decreases within more differentiated
naive T cell subsets. Green cells represent naive T cells, and orange cells represent cells with an effector or memory
phenotype and/or function. Yellow cells represent the intermediate stage seen in Tscm cells. Columns 3–6 correspond to
RTEs, CD31+ naive T cells, CD31− naive T cells and Tscm cells, respectively . The last column of the table is empty as this
column includes many different subsets of T cells, which will have differential marker expression patterns. Table key for
expression or proliferation strength: ++, high; +, medium; +/–, low or absent; –, absent. IL-2Rβ, IL-2 receptor subunit-​β.

Any trigger of activation or proliferation may lead that changes upon environmental stimuli and both
to epigenetic changes in naive T cells; therefore, specific reflects and contributes to functional differentiation of
environments or disease settings may set up naive T cells the T cell response and possibly to the development
for lineage differentiation. In patients with systemic of disease.
lupus erythematosus and those with Sjögren syndrome,
specific disease-​associated methylation patterns of naive Naive T cell characteristics
T cells, which favour T cell differentiation and activa- With the above-​described heterogeneity of naive T cells
tion, have been found35,36. Interestingly, as compared in mind, it is interesting to know to what extent this
with healthy controls, children who later developed translates into heterogeneity in terms of cellular char-
β-​cell autoimmunity had a striking difference in the gene acteristics, such as lifespan, potential to self-​renew and
signature of β-​cell antigen-​specific ‘naive’ (CD45RA+) appearance in different compartments in the body.
T cells, which resembled a pre-​T helper 1 (TH1), TH17
and T follicular helper cell response. This signature Naive T cell dynamics. Within the mouse naive T cell
could be detected in infancy, way before the appearance pool there is some evidence that RTEs have higher death
of any signs of autoimmunity37. Together, these data sug- rates than mature naive T cells38–41 (Fig. 1), although the
gest that naive T cells have a unique epigenetic landscape literature is partially conflicting42. Increased RTE death

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rates may reflect a post-​thymic selection step in which T cells can migrate into nonlymphoid tissues, such as the
part of the RTE pool fails to make the transition to the gut lamina propria, especially early in life47. This capa-
mature naive T cell compartment. In agreement with bility was confirmed in two recent notable studies ana-
this model, it was observed that the TCR repertoires of lysing lymphoid and nonlymphoid tissues of previously
RTEs and mature naive T cells differ43 (Fig. 1). However, healthy, deceased human organ donors46,48. In young
the exact signals that drive RTE maturation and sur- children, CD45RA+CCR7+ naive T cells represented
vival remain elusive7. Recent studies have revealed the predominant T cell population in the blood, spleen
another layer of heterogeneity in the naive T cell pool and draining lymph nodes46,48, and naive T cells were
of mice: despite the high rate of renewal of the naive also observed in mucosal tissues, with frequencies reach-
T cell pool, part of the pool is not replaceable by new ing up to 50% of the tissue-​resident T cells in the lung
cells from the thymus and forms an ‘incumbent’ cell and 60% in the colon46,48. These findings demonstrate
population44. It remains to be investigated whether these that naive T cells are widely distributed among different
incumbent naive T cells possess a special function and tissues early in life.
whether the heterogeneity in cellular death rates that has In adults, the proportion of both CD4+ and CD8+
been observed for mouse naive T cells is also present naive T  cells was lower and decreased with age in
in humans. mucosal tissue, lymph nodes, the spleen and blood46,48.
The upregulation of the activation and tissue-​specific
Tissue compartmentalization. Human T cell-​based T cell marker CD69 on a proportion of human naive
research has been mostly confined to cells obtained CD4+ T cells in lymph nodes and mucosal tissues indi-
from peripheral blood owing to the difficulty of obtain- cated their tissue retention46, which in turn seemed
ing tissue samples. However, the blood contains only to affect their maintenance. TCR clonal distribution
~2–3% of the total T cell pool at any moment in time45. analysis of naive T cells revealed lymphoid tissue site-​
It has recently become clear that naive T cells are far specific clonal expansions of naive T cells in individuals
more compartmentalized than generally appreciated older than 40 years of age, with minimal clonal overlap
and that some cells may hardly even recirculate through with naive T cells from other lymphoid tissue sites. On
the blood46. It has been known for some time that naive the basis of these findings it was proposed that tissue
residency supports the long-​term maintenance of naive
T cells through in situ homeostasis48, which raises the
question of whether naive T cells also adapt to the local
tissue environment, thus further promoting their heter-
CD31+ ogeneity. There is indeed some evidence, based on dif-
Absolute numbers of naive T cells

ferential chemokine receptor and cytokine expression

% of naive T cell population

patterns, that naive CD4+ and CD8+ T cells obtained

RTE from different locations express tissue-​specific signa-
Naive CD4+ tures49. The role of tissues as niches for naive T cell matu-
T cell number ration and maintenance, from RTEs to Tscm cells, remains
unclear and may have important consequences for the
development of (local) vaccination strategies.

Implications for health and disease

It is important to appreciate the heterogeneity of pheno-
type and function among naive T cells when studying the
CD45RA+ TEM cells immune system. Below, we discuss the implications of
Age naive T cell diversity for healthy ageing, neonatal immu-
Neonate Elderly individuals nity, the response to vaccination and application in the
clinical setting of T cell reconstitution following HSCT.
Fig. 2 | Cell dynamics of the different CD45RA CD4 T cell subsets during ageing.
+ +

In neonates, the majority of circulating T cells have a naive phenotype (grey shading,
representing absolute naive T cell numbers) and mostly consist of recent thymic Healthy ageing. It is well known that immune responses
emigrants (RTEs; orange dashed line) and CD31+ naive T cells (red dashed line)17–19,21. to infection and vaccination tend to be impaired in
With the gradual loss of thymopoiesis during ageing, the number of T cells with a naive elderly individuals and that this constitutes a major
phenotype decreases until it reaches a relatively stable number at later age17 ,28,100,101. cause of morbidity and mortality in old age. For example,
A slight decline in the number of naive CD4+ T cells at older ages can become elderly people account for almost 90% of the deaths asso-
considerable in the presence of cytomegalovirus infection14,17 ,102–104. Within the naive ciated with influenza virus infection50 and have a 1,000-
T cell compartment, the fraction of RTEs decreases rapidly whereas the CD31+ fraction fold higher risk of mortality from vaccine-​preventable
diminishes more gradually over time9,14,18,19,105–107. By contrast, the CD31− fraction infections than children51. One of the most important
(purple dashed line) increases over time and encompasses the majority of naive T cells in factors that may be responsible for this impairment is
elderly individuals1,9,17 ,18,107. With the decrease in RTEs and CD31+ naive T cells, the
the progressive decline in thymus output52, which has
fraction of IL-8-producing naive T cells (blue dashed line) also decreases17 ,21. The fraction
of effector memory CD4+ T cells re-​expressing CD45RA (CD45RA+ TEM cells; brown been estimated to decline from an output of ~16 million
dashed line) gradually increases during ageing whereas the proportion of stem cell cells per day in young adults to <1 million cells per day
memory T cells remains relatively stable over time (not shown)96,108. Left y-​axis refers to in adults older than 65 years of age53. As a consequence,
percentage of T cells within naive CD45RA+CD4+ T cells; right y-​axis refers to the composition of the naive T  cell pool changes
absolute naive T cell numbers. considerably with age (Fig. 2).
© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Simpson’s diversity index

It is generally thought that the body responds home- based on measures such as Simpson’s diversity index63 or
A measure of diversity that ostatically to the age-​related loss of thymus output by repertoire skewedness64, which fail to distinguish between
takes into account the number increasing the rate of T cell proliferation and/or decreas- a true loss of T cell clones and the expansion of specific
of clones present, as well as ing the rate of T cell death. Interestingly, there is some evi- clones. As sorted naive T cells may still contain some
the relative abundance of each
dence for cell-​intrinsic increases in naive T cell lifespans memory T cells, and because uneven homeostatic pro-
with age in mice54, as well as increased levels of naive liferation of different naive T cell clones may occur65,
Repertoire skewedness T cell division in humans55 and monkeys56 at an older a reduced diversity score does not necessarily imply a
The extent to which a age. However, it remains to be proved whether increased loss of naive T cell clones. In addition, given that only
repertoire deviates from a
naive T cell division rates in elderly individuals reflect 2–3% of the lymphocyte pool resides in blood, even
situation where all clones occur
equally frequently.
a desirable homeostatic response to thymus involution. blood samples as large as 100 ml (out of a total of the
Notably, a study among very healthy elderly individuals 5 l of blood contained within the human body) repre-
found no evidence for increased T cell division at an older sent only ~0.04% of the total body T cell pool. The naive
age despite a clear reduction in thymus output53. It cannot T cell pool is so immensely diverse that the chance of
be excluded that the increased proliferation rates seen in finding the same clone twice in a small sample of blood
some elderly people may in fact result from shifts in the is extremely low, making it very hard to estimate the total
composition of the naive T cell pool or could even be a diversity. A further complication is that naive T cells that
sign of underlying inflammatory processes53. are found in the blood may not be representative of the
It is quite widely assumed that impaired adaptive naive TCR repertoire at other sites48. Indeed, a study in
immune responses in elderly individuals are partly due aged mice showed that TCR repertoire diversity could
to a loss of naive T cell diversity57–60. Although several undergo an age-​related decrease in spleen-​resident
studies have shown that the diversity of the total T cell naive T cells while remaining fully diverse in the bone
repertoire tends to be lower in elderly individuals61,62, marrow63. The most conclusive study so far revealed only
this could be attributable to expansion of the memory a modest decline in TCR repertoire diversity, by a factor
T cell pool. In fact, there is very little evidence that age- of two to five for both naive CD4+ and CD8+ T cells in
ing leads to true ‘holes’ in the naive T cell repertoire, elderly individuals65, suggesting that reduced immune
and despite great technical advances, measuring the responses are not related to holes in the naive T cell rep-
diversity of the naive T cell pool remains a real chal- ertoire. Alternative explanations may involve the altered
lenge. Most TCR repertoire diversity studies have been functional responsiveness of naive T cells in elderly indi-
viduals because of a shift in the naive T cell spectrum
from RTEs to more mature naive T cells66. In addition,
the age-​related impairment of immune responses may
RTEs also be related to reduced naive T cell functionality due
to epigenetic changes34,67 or even changes in antigen-​
naive T cells presenting cells, which are necessary to trigger a naive
T cell response.
CD31+ Understanding what is causing the decreased
naive T cells
response to vaccination in elderly individuals is crucial
to improve vaccination strategies. If changes in naive
Marker Neonate naive T cells Adult naive T cells T cell diversity or function in elderly individuals are
CD45RA ++ +++ causing the decreased response to vaccination, then it
PTK7* +++ +/– would be prudent to consider vaccinating adults at an
CD31* +++ +/– earlier age. If the functionality and diversity of naive
– ++
T cells in elderly individuals are not limiting factors,
CD25 * dim
vaccine strategies for elderly people may instead have
CD38 +++ +
to focus on boosting the magnitude of the response
CR1 (CD35) and/or CR2 (CD21) ++ +/–
(for example, by the use of different adjuvants).
TLR1 and/or TLR5 ++ +/–
CD154 (CD40L) + +++ Neonatal naive T cells: linking innate and adaptive?
CD93 ++ – Although diminished vaccination responses and
IL-8‡ +++ +/– increased vulnerability to infections are observed in both
IL-2‡ ++ +++ elderly individuals and neonates68, the underlying causes
IFNγ ‡ – ++ differ. In elderly individuals, the T cell compartment is
skewed towards memory; however, the neonatal immune
Fig. 3 | Neonatal versus adult naive T cell characteristics. The majority of neonatal system is skewed towards naivety68. There is emerging
naive T cells express CD31, of which most are recent thymic emigrants (RTEs), whereas in evidence that the lack of memory in neonates is partly
adults only a small fraction of CD31+ naive T cells are RTEs8 (pie charts, top). The compensated for by the fact that neonatal T cells are
difference in composition of the naive T cell compartments is also reflected by
initially skewed towards innate responses and stimuli,
differential phenotypical and functional characteristics3,21,26,109,110 (table, bottom). Table
key for expression strength: +++, very high expression; ++, high expression; +, medium which may have important implications for optimizing
expression; +/–, low or absent expression; –, absent expression. CR , complement neonatal vaccination strategies.
receptor ; PTK7, protein-​tyrosine kinase 7; TLR , Toll-​like receptor . *Only relevant for CD4+ The neonatal T cell compartment mostly consists
naive T cells. ‡Cytokine production assessed after phorbol myristate acetate and of phenotypical naive T cells with a relatively high pro-
ionomycin stimulation. portion of RTEs48 (Fig. 3). As described earlier, RTEs

Nature Reviews | Immunology

© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

produce IL-8, which is an important mediator of still lack CD31 expression. In the following months
the innate immune response 3,21,25. It has been pro- to years, when thymopoiesis is thought to be restored,
posed that IL-8 production by neonatal T cells has the composition of the naive T cell compartment and
a pro-​i nflammatory immuno-​protective function 3. the TCR repertoire diversity of naive T cells slowly
Importantly, IL-8-producing naive T cells have the normalize11,78,79.
capacity to directly convert into IFNγ-​producing TH1 It is widely accepted that lymphopenia induces
cells following proliferation, which reconfirms their alterations in T cell dynamics that speed up immune
responsive phenotype 25. In line with this, neonatal recovery, but it is less clear whether naive T  cell
naive CD8 + T cells proliferate constitutively, pro- dynamics are affected. On the basis of increased
duce antimicrobial peptides and reactive oxygen spe- numbers of TRECs within T cells after HSCT, it has
cies and have a specific gene expression programme been proposed that  thymic output is increased when
with increased (relative to adult naive CD8+ T cells) T cell numbers are low80, although these changes may
Toll-​like receptor 3 (TLR3) and TLR5 expression69. in fact be a natural consequence of the emptiness of
Moreover, neonatal naive T cells appear to be more the T cell pool after HSCT81. Furthermore, increased
susceptible to innate stimuli than adult naive T cells, T cell proliferation rates in HSCT patients are cor-
partly because they are skewed towards RTEs. RTEs related with graft-​versus-​h ost disease (GVHD) and
in general are enriched for the complement receptors infectious-​disease-related complications81, suggest-
CR1 and CR2 and have upregulated expression of ing that increased T cell proliferation does not reflect
TLR1 (REFS. 21,26). Stimulation of neonatal CD4+ T cells a homeostatic response to lymphopenia. Therefore,
with the TLR5 agonist bacterial flagellin or the TLR1 it remains unclear whether human naive T cells are
and TLR2 agonist Pam3Cys further increases IL-8 pro- produced at higher rates when cell numbers are low.
duction, an effect not seen in adult CD4+ T cells3. In Even if naive T cells show a proliferative response
addition, TLR ligand stimulation resulted in the upreg- to lymphopenia, their phenotype and differentia-
ulation of CD45RO and CCR4 in cord-​blood-derived tion programmes may be altered, for example, by
naive T cells but not in adult naive T cells70. These more rapid differentiation within the naive T cell
data suggest that TLR stimulation can directly trigger pool or a skewed response towards the effector T cell
maturation and increase T cell trafficking of neona- and memory T cell pool 77,82, with possible clinical
tal T cells, which implies that innate receptor stim- consequences.
ulation could be used to improve immunization in In HSCT, some inherent characteristics of naive
neonates71,72. Finally, very early in life, naive T cells T cells may be exploited. Following allogeneic HSCT,
become widely distributed and prevalent in periph- alloreactive T cells are enriched in the naive T cell
eral tissues, such as the gut46,48. Thus far, we have little compartment compared with the memory T  cell
idea what this compartmentalization entails. It has compartment; thus, engrafted naive T cells may give
been proposed that, in addition to a possible active rise to graft-​v ersus-tumour (GVT) responses 83,84;
role in fighting local infections, naive T cells in periph- however, naive T cells are also implicated in the inci-
eral tissues may be important for in situ tolerization47. dence of chronic GVHD85,86. Interestingly, cord blood
It remains to be investigated how these cells are main- grafts, which contain a large number of RTEs, induce
tained and activated, whether and how they differentiate low rates of GVHD without compromising the GVT
and migrate and whether they exert any local effector effect 87. The challenge is to determine the optimal
functions. balance between depletion and functional recovery of
Together, the unique innate profile and distribution the T cell compartment. Research is complicated by
of neonatal naive T cells seems to reflect the tempo- numerous interlinked factors that may affect T cell
ral transition of host defence from innate to adaptive recovery, including the source of the graft (cord blood
immunity and may provide opportunities for early-​life or bone marrow, allogeneic or autologous), graft
immunization. manipulation, conditioning regimens, post-​transplan-
tation treatment, cytomegalovirus seropositivity of
Immune reconstitution following haematopoietic either the donor or recipient, age of the graft recipient
stem cell transplantation. HSCT, a key treatment for and treatment-​related thymus damage. One of the crit-
numerous malignant and nonmalignant disorders, is ical outstanding issues is whether the functional heter-
followed by a phase of profound lymphopenia. T cell ogeneity of naive T cells is important in these settings.
Thymic output
The amount of T cells that
recovery after HSCT is critical for long-​term survival, For example, if naive T cell numbers reach normal
successfully exit the thymus but qualitative and quantitative reconstitution of the levels after HSCT, but with a strong skewing towards a
into the periphery after naive T cell compartment is a very slow process, which more differentiated phenotype, can this be considered
intrathymic selection. typically takes months to years73,74 (Fig. 4). In the first a functional recovery? Do engrafted RTEs behave dif-
weeks to months after HSCT, the proliferation rate of ferently from mature naive T cells? Combinations of
Graft-​versus-host disease
(GVHD). An inflammatory naive T cells is typically increased, clonal expansions different techniques, such as TREC content measure-
complication following the occur and TCR diversity is reduced 75. In addition, ments, TCR sequencing, CyTOF (multiparameter mass
transplantation of stem cells or Tscm cells constitute a major portion of T cells in the cytometry) and functional assays will provide further
organs to a genetically different blood76,77. Within the following months after HSCT, the mechanistic insights. In addition, standardized and
person caused by donor
immune cells that recognize
proportion of Tscm cells present in the blood decreases extensive phenotypic measurements of T cell recon-
the recipient’s cells and tissues back to normal levels and the naive T cell pool slowly stitution, including the different naive T cell subsets,
as foreign. reconstitutes, although the majority of naive T cells will be an important step forward in mapping T cell
© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Effector T cell
Naive CD31– CD31+
and/or memory Tscm cells
T cells naive T cells naive T cells
T cells subsets


Lymphopenia-induced proliferation Thymopoiesis

T cell numbers

Days–weeks Months Months–years

TCR diversity

Proliferation + +++ ++

Fig. 4 | Naive T cell characteristics following haematopoietic stem cell transplantation. Before haematopoietic
stem cell transplantation (HSCT), the proportion of the different naive T cell subsets is in part dependent on age, the
naive T cell pool contains a relatively broad T cell receptor (TCR) diversity and naive T cells undergo slow rates of
proliferation. Following conditioning, T cell numbers drastically drop, proliferation and clonal expansion of surviving
and/or donor T cells increase and TCR diversity decreases75. During the first days to weeks after HSCT , stem cell
memory T (Tscm) cells constitute a major proportion of the T cells in the blood, whereas naive T cells can hardly be
detected76,77. Within the following months, the proportion of Tscm cells decreases again and the naive T cell pool slowly
starts to reconstitute, although the majority of naive T cells still lack CD31 expression. In the following months to
years, thymopoiesis is thought to be restored, and the composition as well as the TCR repertoire diversity of the naive
T cell pool slowly normalizes11,78,79. Full reconstitution of the T cell pool to resemble the situation before HSCT typically
takes months to years or may not even occur at all, and it depends on many factors, including age, thymic function,
conditioning regime and stem cell source75. Peripheral blood CD8+ T cells may reach normal levels as early as 3–6
months after HSCT, whereas a substantially longer period is necessary for normalization of CD4+ T cell numbers111,112.
T cell proliferation key: +++, high; ++, medium; +, low .

reconstitution and relating it to treatment regimens further identification of different subsets within the
and outcome. naive T cell compartment; this could have important
clinical implications for immune monitoring and
Concluding remarks intervention strategies and shed further light on the
Current assessments that are commonly used to exam- topic of predifferentiation of naive T cells. The iden-
ine the human naive T cell compartment often include tification of naive T cell subsets should also extend
multiple T cell subsets, which may not be reflective to peripheral tissue sites outside the circulation, and
of the true naive T cell pool; this may compromise future research may reveal specific niches for naive
phenotypical and functional analyses, especially when T cell maintenance and functional differentiation.
performed under nonhomeostatic conditions or on It remains to be determined whether the innate bias
samples from ageing subjects. Additionally, there and tissue location of neonatal naive T cells also have
is compelling evidence that within the naive T cell functional consequences.
compartment there is heterogeneity regarding phe- Taken together, looking beyond the seemingly calm
notype, anatomic localization, proliferation, survival, surface of naive T cells may reveal aspects that can guide
cytokine production and gene expression profiles. strategies for optimizing vaccinations, immune recovery
With the increased availability of multiparameter and healthy ageing.
assays, such as mass cytometry (CyTOF) and single-​
Published online xx xx xxxx
cell RNA sequencing, it is expected that there will be

Nature Reviews | Immunology

© 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

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