REVIEW
◥IMMUNOLOGY
Early-life imprinting of unconventional T cells
and tissue homeostasis
Michael G. Constantinides^1 and Yasmine Belkaid1,2
Unconventional T cells—including invariant natural killer T (iNKT) cells, mucosal-associated
invariant T (MAIT) cells, and defined subsets ofgdT cells—are restricted by monomorphic major
histocompatibility complex class Ib (MHC-Ib) molecules and seed tissues during development.
Early-life instructive signals, including those derived from the microbiota, establish homeostatic set
points for unconventional T cells, a phenomenon that has lifelong consequences for the regulation
of tissue immunity, inflammation, and repair. Unconventional T cells compete for niches within
tissues, and recent evidence supports the idea that the fundamental role of these cells in tissue
physiology may result from their action as a network with overlapping and potentially synergistic
functions, rather than as individual subsets.
T
he immune system, previously appre-
ciated for its role in antimicrobial pro-
tection, is now known to also govern
numerous aspects of host physiology ( 1 ).
Part of this control occurs through the
coordinated action of tissue-resident lympho-
cytes, including unconventional T cells that
accumulate in response to specific develop-
mental cues and exposure to defined antigens.
Although conventional T cells recognize pep-
tides presented by polymorphic major histo-
compatibility complex (MHC) proteins, a large
proportion of T cells within tissues are specific
for modified peptides and small molecules,
including defined lipids and metabolites pro-
duced by microbes ( 2 ). These unconventional
T cells are restricted by monomorphic MHC
class Ib (MHC-Ib) molecules; some popula-
tions, such as invariant natural killer T (iNKT)
cells, mucosal-associated invariant T (MAIT)
cells, and subsets ofgdT cells, express a semi-
invariant T cell receptor (TCR) that limits their
antigenic range analogously to an innate im-
mune receptor ( 2 ) (Table 1). Termed innate-
like T cells, these populations developmentally
acquire effector characteristics prior to thymic
egress, including rapid cytokine release and
expression of chemokine receptors and integrins,
which results in their accumulation in tissues
earlier than conventional effector T cells, during
the second trimester in humans and within
3 weeks of birth in mice ( 3 – 8 ). This dependence
on early-life signals raises fundamental ques-
tions regarding the extent to which the early
emergence of unconventional T cells may pro-
vide critical functions before the establish-
ment of classical immunologic memory. The
evolutionary conservation of many MHC-Ib
molecules suggests that unconventional T cells
may serve a critical role in host physiology, par-
ticularly in mediating the interaction with the
microbiota and maintaining tissue homeosta-
sis (Fig. 1). Recent evidence also supports the
idea that unconventional T cells compete for
niches within tissues and may exert overlap-
ping functions associated with the preservation
of tissue homeostasis. We discuss the identi-
fication of signals responsible for the devel-
opment of unconventional T cells and their
accumulation within tissues, and how alter-
ations in early-life signals or inflammatory
challenges can imprint the unconventional
T cell network and affect tissue homeostasis
for the long term.Dependence on early-life signals: Microbiota
and epithelially derived signals
Barrier tissues are the primary route of ex-
posure to the microbiota and are enriched in
unconventional T cells (Fig. 2). The ability of
MHC-Ib molecules to present antigens with
specific chemical moieties or amino acid se-
quences, which can be derived from a large
constituency of the microbiota, places immune
cells that recognize them as ideal candidates
for the constitutive sensing and recognition
of microbial antigens. Indeed, recent evidence
suggests that unconventional T cells, in ad-
dition to using microbiota-derived metabolites
for their development and function, may also
contribute to the beneficial dialog between the
microbiota and its host.
Innate-like T cell subsets acquire effector
characteristics prior to thymic egress, which
results in their accumulation in tissues during
earlylife( 3 – 8 ). Studies of iNKT cells provided
the first demonstration that early-life exposure
to the microbiota controls the development
and tissue accumulation of unconventional
T cells. iNKT cells express a semi-invariant
TCRa-chain that enables them to recognize
both endogenous and microbial lipids pre-
sented by CD1d ( 9 ). Although iNKT cells can
be selected on self-ligands ( 10 ), they are hypo-
responsive in the absence of commensals, and
germ-free (GF) mice exhibit fewer iNKT cells
in the thymus, spleen, and liver ( 11 , 12 ). How-
ever, iNKT cells accumulate within the colonic
lamina propria and lungs of GF mice as a con-
sequence of elevated expression of the chemo-
kine CXCL16 by epithelial cells, exacerbating
colonic inflammation and allergic airway re-
sponses ( 13 ). Although theCxcl16gene is hyper-
methylated in the absence of commensals,
colonization of neonatal GF mice diminishes
DNA methylation, abrogating CXCL16 produc-
tion and preventing the subsequent recruit-
ment of iNKT cells ( 13 ). Conversely, microbialRESEARCH
Constantinides and Belkaid,Science 374 , eabf0095 (2021) 10 December 2021 1of6
(^1) Metaorganism Immunity Section, Laboratory of Immune
System Biology, National Institute of Allergy and Infectious
Diseases, Bethesda, MD 20892, USA.^2 NIAID Microbiome
Program, National Institute of Allergy and Infectious
Diseases, Bethesda, MD 20892, USA.
*Corresponding author. Email: [email protected]
(M.G.C.); [email protected] (Y.B.)
Present address: Department of Immunology and Microbiology,
Scripps Research, La Jolla, CA 92037, USA.
Table 1. Unconventional T cells.Populations of unconventional T cells present in humans (h) and
mice (m) are listed, with innate-like T cell subsets in boldface. DETC, dendritic epidermal T cell;
IEL, intraepithelial lymphocyte; GEM, germline-encoded mycolyl-reactive.
Population MHC-Ib Antigen TCR repertoire
gd.....................................................................................................................................................................................................................17 T Unknown Unknown Vg4orVg6 (m)
DETC (m).....................................................................................................................................................................................................................Unknown Unknown Vg5Vd1 (m)
gd.....................................................................................................................................................................................................................IEL Unknown Butyrophilin-like molecules Vg4 (h), Vg7 (m)
MAIT MR1 Microbial metabolites
Va7.2 Ja33/20/12 (h)
.....................................................................................................................................................................................................................Va19 Ja33 (m)
iNKT CD1d Glycolipids
Va24 Ja18 (h)
.....................................................................................................................................................................................................................Va14 Ja18 (m)
GEM (h).....................................................................................................................................................................................................................CD1b Glycolipids Va7.2 Ja9 (h)
T.....................................................................................................................................................................................................................C 1 Qa1 (m) Peptides Polyclonal
Type II NKT.....................................................................................................................................................................................................................CD1d Glycolipids Polyclonal
T.....................................................................................................................................................................................................................C1/17 H2-M3 (m) N-formylated peptides Polyclonal