Science - USA (2022-06-03)

NF-kB signaling accompanying ABT(entry) to
thymic mature T cells, expression of NF-kB-
signaling genes continued to increase when
mature T cells migrate out to peripheral tis-
sues (Fig. 3E).

System-wide blood and immune cell development

While examining the distribution of various
cell types across different organ systems, we

were surprised to find that lineage-committed

hematopoietic progenitors were present in

nonhematopoietic organs. In particular, we

detected B cell progenitors in almost all pre-

natal organs, megakaryocyte/erythroid progen-

itors in developing spleen and skin, and

myeloid progenitors in the thymus, spleen,

skin,andkidney(Fig.4A).Bycontrast,Tcell

progenitors were restricted to the thymus, po-

tentially reflecting more stringent niche require-

ments for T cell development and consistent

with the observed absence of T cells in chil-

dren with congenital athymia ( 37 ). This finding

suggests that hematopoiesis is not restricted

to developing liver and bone marrow between

7and17pcw( 38 ) and that other organs can

also support blood and immune cell differen-

tiation during prenatal development.

Suoet al., Science 376 , eabo0510 (2022) 3 June 2022 5of15

B

D

E

C

Thymus Spleen Gut Skin

Nhood size

100

150

200

250

300

3

4

5

6

Organ

enrichment

(logFC)

ABT(ENTRY)

CD4+T CD8+T

CD8AA

TREG

TYPE_1_INNATE_T

TYPE_3_INNATE_T

Nhood

graph 1

Nhoodgraph 2

Thymus other

Interf

eron

alpha response

TNF signalin

g

via NF

B

ABT(ENTR

Y)

CD4+TCD8+TCD8AATREG

TYPE_1_INNA

TE_T

TYPE_3_INNATE_T

CD4+TCD8+TTREG

TYPE_1_INNATE_TTYPE_3_INNA

TE_T

CD8A

CD4

TOX2

IFIT3

PARP9

CMPK2DDX60

PLSCR1LAMP3

LGALS3BP

KLF2

JUNB

FOSBSIK1

SOCS3PLEK

NR4A2 −1^0

1

2

Scaled mean

expression

markergenes

DE genes

Neighborhood annotation

7 PCW 17 PCW 12 PCW17 PCW 7 PCW 17 PCW 9 PCW17 PCW 7 PCW 16 PCW

Liver Bone Marrow Thymus Spleen Skin

NK cells

ILCs

B cells

Developing

T cells

Conventional

SP T cells

Unconventional

SP T cells

−1 0 1 −2 −1 0 12 −2 −1 0 1 2 −2 −1 0 1 2 3−1 0 1

CYCLING_NKNK

CYCLING_ILC

ILC3ILC2

CYCLING_BB1

IMMATURE_BMATURE_B

SMALL_PRE_BLARGE_PRE_B

LATE_PRO_BPRO_B

PRE_PRO_B

ABT(ENTRY)DP(Q)_T

DP(P)_T

DN(Q)_TDN(P)_T

DN(early)_T

TREG

CD8+TCD4+T

CYCLING_T

TYPE_3_INNATE_TCD8AA

TYPE_1_INNATE_T

log-Fold Change in abundance over time

Liver Skin Bone Marrow Thymus Spleen

TNF signaling

Inflammatory

response

Immune

function

< 8pcw< 10pcw< 12pcw< 14pcw< 16pcw< 18pcw< 8pcw< 10pcw< 12pc

w

< 14pc

w

< 16pc

w

< 18pc

w

< 8pcw< 10pcw< 12pcw< 14pc

w

< 16pcw< 18pcw< 8pcw< 10pc

w

< 12pc

w

< 14pcw< 16pcw< 18pcw< 8pcw< 10pcw< 12pcw< 14pc

w

< 16pcw< 18pcw

SGK1

RHOB

REL

NFKBIA

NFKB1KLF6

KLF2

KDM6B

IER5

ICAM1

FOSB

FOS

DUSP4

DUSP1

DNAJB4

CXCL3

CEBPDCD83

CD44

BIRC3

AT F 3

RGS16

EMP3

CD70

CD48

CCR7

TIGIT

SLA2

ITGA4

IL10

GZMB

CD200R1CLEC2B

CCL4L2

Age bins

DEGs

Scaled mean expression

−2 −1 0 123

A

TNF signaling

via NFB

type I

interferon

signaling

Fig. 3. Lymphoid variation across time and tissues.(A) Bee-swarm plot of
log-fold change (x-axis) in cell abundance across gestational stages in Milo
neighborhoods of lymphoid cells (as in Fig. 2A). (B) Heatmap showing average
expression across time of a selection of genes identified as markers of early-
specific and late-specific NK neighborhoods (as in Fig. 2B): NK cells identified in
liver and skin before 12 pcw express TNF proinflammatory genes, whereas the
expression of immune-effector genes such as cytokines, chemokines, and
granzyme genes increases after 12 pcw. Age bins in which <30 NK cells were
present in a given organ are grayed out. (C) Close-up view of single-positive
T cells on Milo neighborhood embedding of lymphoid cells. Each point represents
a neighborhood, and the layout of points is determined by the position of the

neighborhood index cell in the UMAP in fig. S4I. Top: neighborhoods are colored

by the cell population they overlap. Bottom: neighborhoods are colored by

their log-fold change in abundance between the specified organ and all other

organs. Only neighborhoods displaying significant differential abundance

(spatialFDR < 10%) are colored. (D) Mean expression of a selection of

differentially expressed genes between single-positive T cells from thymus (TH)

and other organs. Genes down-regulated in the thymus associated with TNF

signaling (using MSigDB Hallmark 2020 gene sets) and genes up-regulated in the

thymus associated with an IFN-aresponse are shown. (E) Schematic of the

proposed mechanism of thymocyte maturation and egression from thymus

mediated by type I IFN and NF-kB signaling.

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