Genome biology,
Journal Year:
2022,
Volume and Issue:
23(1)
Published: Oct. 17, 2022
Abstract
Background
Cell-cell
interactions
are
important
for
information
exchange
between
different
cells,
which
the
fundamental
basis
of
many
biological
processes.
Recent
advances
in
single-cell
RNA
sequencing
(scRNA-seq)
enable
characterization
cell-cell
using
computational
methods.
However,
it
is
hard
to
evaluate
these
methods
since
no
ground
truth
provided.
Spatial
transcriptomics
(ST)
data
profiles
relative
position
cells.
We
propose
that
spatial
distance
suggests
interaction
tendency
cell
types,
thus
could
be
used
evaluating
tools.
Results
benchmark
16
by
integrating
scRNA-seq
with
ST
data.
characterize
into
short-range
and
long-range
distributions
ligands
receptors.
Based
on
this
classification,
we
define
enrichment
score
apply
an
evaluation
workflow
tools
15
simulated
5
real
datasets.
also
compare
consistency
results
from
single
commonly
identified
interactions.
Our
suggest
predicted
highly
dynamic,
statistical-based
show
overall
better
performance
than
network-based
ST-based
Conclusions
study
presents
a
comprehensive
scRNA-seq.
CellChat,
CellPhoneDB,
NicheNet,
ICELLNET
other
terms
software
scalability.
recommend
at
least
two
ensure
accuracy
have
packaged
detailed
documentation
GitHub
(
https://github.com/wanglabtongji/CCI
).
Nature,
Journal Year:
2023,
Volume and Issue:
619(7971), P. 801 - 810
Published: July 12, 2023
The
function
of
a
cell
is
defined
by
its
intrinsic
characteristics
and
niche:
the
tissue
microenvironment
in
which
it
dwells.
Here
we
combine
single-cell
spatial
transcriptomics
data
to
discover
cellular
niches
within
eight
regions
human
heart.
We
map
cells
microanatomical
locations
integrate
knowledge-based
unsupervised
structural
annotations.
also
profile
cardiac
conduction
system
Nature,
Journal Year:
2023,
Volume and Issue:
616(7955), P. 143 - 151
Published: March 29, 2023
Abstract
The
relationship
between
the
human
placenta—the
extraembryonic
organ
made
by
fetus,
and
decidua—the
mucosal
layer
of
uterus,
is
essential
to
nurture
protect
fetus
during
pregnancy.
Extravillous
trophoblast
cells
(EVTs)
derived
from
placental
villi
infiltrate
decidua,
transforming
maternal
arteries
into
high-conductance
vessels
1
.
Defects
in
invasion
arterial
transformation
established
early
pregnancy
underlie
common
disorders
such
as
pre-eclampsia
2
Here
we
have
generated
a
spatially
resolved
multiomics
single-cell
atlas
entire
maternal–fetal
interface
including
myometrium,
which
enables
us
resolve
full
trajectory
differentiation.
We
used
this
cellular
map
infer
possible
transcription
factors
mediating
EVT
show
that
they
are
preserved
vitro
models
differentiation
primary
organoids
3,4
stem
5
define
transcriptomes
final
cell
states
invasion:
bed
giant
(fused
multinucleated
EVTs)
endovascular
EVTs
(which
form
plugs
inside
arteries).
predict
cell–cell
communication
events
contributing
formation,
model
dual
role
interstitial
Together,
our
data
provide
comprehensive
analysis
postimplantation
can
be
inform
design
experimental
placenta
Science,
Journal Year:
2024,
Volume and Issue:
383(6679)
Published: Jan. 11, 2024
Neutrophils
are
increasingly
recognized
as
key
players
in
the
tumor
immune
response
and
associated
with
poor
clinical
outcomes.
Despite
recent
advances
characterizing
diversity
of
neutrophil
states
cancer,
common
trajectories
mechanisms
governing
ontogeny
relationship
between
these
remain
undefined.
Here,
we
demonstrate
that
immature
mature
neutrophils
enter
tumors
undergo
irreversible
epigenetic,
transcriptional,
proteomic
modifications
to
converge
into
a
distinct,
terminally
differentiated
dcTRAIL-R1
Nature Biotechnology,
Journal Year:
2022,
Volume and Issue:
41(3), P. 332 - 336
Published: Oct. 27, 2022
Abstract
Models
of
intercellular
communication
in
tissues
are
based
on
molecular
profiles
dissociated
cells,
limited
to
receptor–ligand
signaling
and
ignore
spatial
proximity
situ.
We
present
node-centric
expression
modeling,
a
method
graph
neural
networks
that
estimates
the
effects
niche
composition
gene
an
unbiased
manner
from
profiling
data.
recover
signatures
processes
known
underlie
cell
communication.
Nature Communications,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: March 21, 2023
Abstract
Spatial
transcriptomics
technologies
are
used
to
profile
transcriptomes
while
preserving
spatial
information,
which
enables
high-resolution
characterization
of
transcriptional
patterns
and
reconstruction
tissue
architecture.
Due
the
existence
low-resolution
spots
in
recent
technologies,
uncovering
cellular
heterogeneity
is
crucial
for
disentangling
cell
types,
many
related
methods
have
been
proposed.
Here,
we
benchmark
18
existing
resolving
a
deconvolution
task
with
50
real-world
simulated
datasets
by
evaluating
accuracy,
robustness,
usability
methods.
We
compare
these
comprehensively
using
different
metrics,
resolutions,
spot
numbers,
gene
numbers.
In
terms
performance,
CARD,
Cell2location,
Tangram
best
conducting
task.
To
refine
our
comparative
results,
provide
decision-tree-style
guidelines
recommendations
method
selection
their
additional
features,
will
help
users
easily
choose
fulfilling
concerns.
Cell,
Journal Year:
2022,
Volume and Issue:
185(25), P. 4841 - 4860.e25
Published: Dec. 1, 2022
We
present
a
multiomic
cell
atlas
of
human
lung
development
that
combines
single-cell
RNA
and
ATAC
sequencing,
high-throughput
spatial
transcriptomics,
imaging.
Coupling
methods
with
analysis
has
allowed
comprehensive
cellular
survey
the
epithelial,
mesenchymal,
endothelial,
erythrocyte/leukocyte
compartments
from
5–22
post-conception
weeks.
identify
previously
uncharacterized
states
in
all
compartments.
These
include
developmental-specific
secretory
progenitors
subtype
neuroendocrine
related
to
small
cancer.
Our
datasets
are
available
through
our
web
interface
(https://lungcellatlas.org).
To
illustrate
its
general
utility,
we
use
generate
predictions
about
cell-cell
signaling
transcription
factor
hierarchies
which
rigorously
test
using
organoid
models.
