Cell Reports Medicine,
Journal Year:
2023,
Volume and Issue:
4(10), P. 101231 - 101231
Published: Oct. 1, 2023
Neoadjuvant
chemotherapy
(NAC)
for
rectal
cancer
(RC)
shows
promising
clinical
response.
The
modulation
of
the
tumor
microenvironment
(TME)
by
NAC
and
its
association
with
therapeutic
response
remain
unclear.
Here,
we
use
single-cell
RNA
sequencing
spatial
transcriptome
to
examine
cell
dynamics
in
29
patients
RC,
who
are
sampled
pairwise
before
after
treatment.
We
construct
a
high-resolution
cellular
dynamic
landscape
remodeled
their
associations
markedly
reshapes
populations
cancer-associated
fibroblasts
(CAFs),
which
is
strongly
associated
CAF
subsets
regulate
TME
through
recruitment
crosstalk
activate
immunity
suppress
progression
multiple
cytokines,
including
CXCL12,
SLIT2,
DCN.
In
contrast,
epithelial-mesenchymal
transition
malignant
cells
upregulated
CAF_FAP
MIR4435-2HG
induction,
resulting
worse
outcomes.
Our
study
demonstrates
that
inhibits
modulates
remodeling
CAFs.
Cell,
Journal Year:
2024,
Volume and Issue:
187(8), P. 1990 - 2009.e19
Published: March 20, 2024
Multiple
sclerosis
(MS)
is
a
neurological
disease
characterized
by
multifocal
lesions
and
smoldering
pathology.
Although
single-cell
analyses
provided
insights
into
cytopathology,
evolving
cellular
processes
underlying
MS
remain
poorly
understood.
We
investigated
the
dynamics
of
modeling
temporal
regional
rates
progression
in
mouse
experimental
autoimmune
encephalomyelitis
(EAE).
By
performing
spatial
expression
profiling
using
situ
sequencing
(ISS),
we
annotated
neighborhoods
found
centrifugal
evolution
active
lesions.
demonstrated
that
disease-associated
(DA)-glia
arise
independently
are
dynamically
induced
resolved
over
course.
Single-cell
mapping
human
archival
spinal
cords
confirmed
differential
distribution
homeostatic
DA-glia,
enabled
deconvolution
inactive
sub-compartments,
identified
new
lesion
areas.
establishing
resource
neuropathology
at
resolution,
our
study
unveils
intricate
MS.
Nature Cell Biology,
Journal Year:
2024,
Volume and Issue:
26(9), P. 1613 - 1622
Published: Sept. 1, 2024
The
growing
availability
of
single-cell
and
spatially
resolved
transcriptomics
has
led
to
the
development
many
approaches
infer
cell-cell
communication,
each
capturing
only
a
partial
view
complex
landscape
intercellular
signalling.
Here
we
present
LIANA+,
scalable
framework
built
around
rich
knowledge
base
decode
coordinated
inter-
intracellular
signalling
events
from
single-
multi-condition
datasets
in
both
data.
By
extending
unifying
established
methodologies,
LIANA+
provides
comprehensive
set
synergistic
components
study
communication
via
diverse
molecular
mediators,
including
those
measured
multi-omics
is
accessible
at
https://github.com/saezlab/liana-py
with
extensive
vignettes
(
https://liana-py.readthedocs.io/
)
an
all-in-one
solution
inference.
Genome Medicine,
Journal Year:
2024,
Volume and Issue:
16(1)
Published: Jan. 18, 2024
Abstract
Spatial
multi-omic
studies
have
emerged
as
a
promising
approach
to
comprehensively
analyze
cells
in
tissues,
enabling
the
joint
analysis
of
multiple
data
modalities
like
transcriptome,
epigenome,
proteome,
and
metabolome
parallel
or
even
same
tissue
section.
This
review
focuses
on
recent
advancements
spatial
multi-omics
technologies,
including
novel
computational
approaches.
We
discuss
low-resolution
high-resolution
methods
which
can
resolve
up
10,000
individual
molecules
at
subcellular
level.
By
applying
integrating
these
techniques,
researchers
recently
gained
valuable
insights
into
molecular
circuits
mechanisms
govern
cell
biology
along
cardiovascular
disease
spectrum.
provide
an
overview
current
approaches,
with
focus
integration
datasets,
highlighting
strengths
weaknesses
various
pipelines.
These
tools
play
crucial
role
analyzing
interpreting
facilitating
discovery
new
findings,
enhancing
translational
research.
Despite
nontrivial
challenges,
such
need
for
standardization
experimental
setups,
analysis,
improved
tools,
application
holds
tremendous
potential
revolutionizing
our
understanding
human
processes
identification
biomarkers
therapeutic
targets.
Exciting
opportunities
lie
ahead
field
will
likely
contribute
advancement
personalized
medicine
diseases.
Genome biology,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: Jan. 12, 2024
Abstract
Existing
methods
for
analysis
of
spatial
transcriptomic
data
focus
on
delineating
the
global
gene
expression
variations
cell
types
across
tissue,
rather
than
local
changes
driven
by
cell-cell
interactions.
We
propose
a
new
statistical
procedure
called
niche-differential
(niche-DE)
that
identifies
cell-type-specific
niche-associated
genes,
which
are
differentially
expressed
within
specific
type
in
context
niches.
further
develop
niche-LR,
method
to
reveal
ligand-receptor
signaling
mechanisms
underlie
patterns.
Niche-DE
and
niche-LR
applicable
low-resolution
spot-based
transcriptomics
is
single-cell
or
subcellular
resolution.
