T cells could be subdivided into a subset en-
riched in the thymus and other subsets en-
riched in peripheral organs (Fig. 3C). Thymic
mature T cells overexpressed genes involved in

interferon-a(IFN-a) signaling, whereas periph-

eral mature T cells had higher expression of

genes associated with TNF and NF-kBsignal-

ing (Fig. 3D, fig. S19B, and table S4). Both path-

ways have been implicated in the last stages of

functional maturation of murine T cells right

before emigration out of the thymus ( 35 , 36 ).

In addition to the increase in type I IFN and

Suoet al., Science 376 , eabo0510 (2022) 3 June 2022 4of15

A

B

C

E

Neighborhood annotation

MONOCYTE_I_CXCR4

MONOCYTE_III_IL1B MONOCYTE_II_CCR2

PROMONOCYTE

Nhood

graph 1

Nhoodgraph 2

Skin Spleen

Bone Marrow Liver

Nhood size

(^100150)
(^200250)
300
3
4
5
Organ
enrichment
(logFC)
D
−1
0
1
Scaled mean
expression
BM other
markergenes
G2/M checkpoin
t
TNF signaling
via NF
B
MONOI
CX
CR4
MO
NO_II
_CCR2
MO
NO_I
I_CC
R2
MO
NO_I
II_IL
1B
IL1B
CCR2
CXCR4
MCM2
AURKB
MNAT1
NSD2
DTYMK
CENPF
UCK2
CCNB2
GINS2
TOP2A
CDC20
PNRC1
SOD2
HES1
G0S2
TRIP10
PLAUR
DE genesIL1B
Liver Bone Marrow Thymus Spleen Skin
Progenitors
DCs
Granulocytes
Mono
MACs
−1 0 1 −3 −2 −1 0 1 2 −1 0 1 2 −2 −1 0 12 −1 0 1
PROMYELOCYTEMYELOCYTE
PROMONOCYTECYCLING_MPP
CYCLING_MEMPMEP
MEMP
LMPP_MLPMOP
GMP
HSC_MPPCMP
CYCLING_PDCPDC
MIGRATORY_DC
CYCLING_DCDC2
PRE_DC2DC1
EOSINOPHIL_BASOPHILMAST_CELL
NEUTROPHIL
MONOCYTE_II_CCR2MONOCYTE_III_IL1B
MONOCYTE_I_CXCR4
LANGERHANS_CELLSOSTEOCLAST
MACROPHAGE_KUPFFER_LIKEMACROPHAGE_TREM2
MACROPHAGE_IRON_RECYCLING
MACROPHAGE_LYVE1_HIGHMACROPHAGE_MHCII_HIGH
MACROPHAGE_PROLIFERATING
log-Fold Change in abundance over time
7 PCW 17 PCW 12 PC
W
17 PCW^7 PCW 17 PCW 9 PC
W
17 P
CW
7 PC
W
16 PCW
TREM2 LYVE1_HIGH PROLIFERATINGIRON_RECYCLING MHCII_HIGH KUPFFER_LIKE
0.00
0.25
0.50
0.75
1.00
Fraction ofMacrophages
TREM 2 LYVE1_HIGH PROLIFERATINGIRON_RECYCLING MHCII_HIGH KUPFFER_LIKE
iron
recycling
proinflammatory
immune
development
antigen
presentation
< 8pcw< 14pcw<^8 pcw< 10pc
w
< 12pc
w
< 14p
cw
< 16
pcw
< 18pcw<
8pcw
< 1
0pcw
< 12p
cw
< 14pcw< 16
pcw
< 18
pcw< 8pcw
< 10
pcw
< 12pcw< 14pcw< 16
pcw
<^1
8pcw< 8pcw
< 10pcw< 12
pcw
< 14pc
w
< 16pcw< 1
8pc
w
< 8pc
w
< 1
0pcw
< 12pcw< 14
pcw
< 16pcw< 18pcw
BLVRB
HMOX1
IL1B
NFKBIA
CXCL8
CCL4
CCL3
TNF
CCL3L1
CCL4L2
IL1A
NAMPT
IFIT2
MARCO
FPR2
FPR3
C5AR1
HLA−DPA1
HLA−DRA
HLA−DRB5
Age bins
DEG
s

cells

2500 5000 7500 10000 12500
organ
YS
LI
SK
SP
BM
GU
Scaled mean expression
−2 0 2
MATURE
MONOCYTES
BONE MARROW OTHER ORGANS
Fig. 2. Myeloid 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 myeloid cells. Results from five organs are shown. Neighborhoods overlapping the
same cell population are grouped together (y-axis) and colored if displaying
significant differential abundance (DA) (spatial FDR < 10%). The black dot denotes
the median log-fold change. The top bar denotes the range of gestational stages
of the organ samples analyzed. (B) Heatmap of average expression across time of
a selection of markers of stage-specific macrophage neighborhoods. Mean log-
normalized expression for each gene is scaled (z-score). Gestational ages are
grouped in six age bins. Age bins in which <30 cells of a given subset were present
are not shown. The top panel shows the fraction of all macrophages belonging to
the specified macrophage population in each time point and each organ (color).
(C) Close-up view of monocytes on Milo neighborhood embedding of myeloid cells
(subset from fig. S16). Top: neighborhoods are colored byoverlappingcell
population. Bottom: neighborhoods displaying significant DA (spatialFDR < 10%) are
colored by log-fold change in abundancebetween the specified organ and all
other organs. (D)Meanexpressionofaselectionof differentially expressed genes
between CCR2himonocytes from bone marrow (BM) and other organs. Log-normalized
expression for each gene is scaled (z-score). Genes up-regulated in bone marrow
associated with G 2 /M checkpoint and genes down-regulated in bone marrow
associated with TNF signaling are shown(from MSigDB Hallmark 2020 gene sets).
(E) Schematic of the proposed process of monocyte egression from the bone
marrow mediated by CXCR4 and CCR2 expression: CXCR4himonocytes are retained
in the bone marrow until they switch to a proliferative state with increased
expression of CCR2, mediating tissue egression. CCR2himonocytes seed peripheral
tissues and then mature further to the periphery-specific IL1B-expressing subtype.
RESEARCH | RESEARCH ARTICLE