Experimental & Molecular Medicine,
Год журнала:
2023,
Номер
55(10), С. 2105 - 2115
Опубликована: Окт. 2, 2023
Abstract
The
brain
is
one
of
the
most
complex
living
tissue
types
and
composed
an
exceptional
diversity
cell
displaying
unique
functional
connectivity.
Single-cell
RNA
sequencing
(scRNA-seq)
can
be
used
to
efficiently
map
molecular
identities
various
in
by
providing
transcriptomic
profiles
individual
cells
isolated
from
tissue.
However,
lack
spatial
context
scRNA-seq
prevents
a
comprehensive
understanding
how
different
configurations
give
rise
specific
functions
regions
each
distinct
connected
form
unit.
To
understand
contribute
functions,
it
crucial
correlate
obtained
through
with
their
information
intact
Spatial
transcriptomics
(ST)
resolve
organization
Various
ST
tools
developed
during
past
decade
based
on
imaging
technology
have
permitted
creation
atlases
pulled
properties
neural
circuits
into
ever-sharper
focus.
In
this
review,
we
present
summary
several
applications
neuroscience
discuss
unprecedented
insights
these
made
possible.
Cancer-associated
fibroblasts
(CAFs)
are
a
heterogeneous
cell
population
that
plays
crucial
role
in
remodeling
the
tumor
microenvironment
(TME).
Here,
through
integrated
analysis
of
spatial
and
single-cell
transcriptomics
data
across
six
common
cancer
types,
we
identified
four
distinct
functional
subgroups
CAFs
described
their
distribution
characteristics.
Additionally,
RNA
sequencing
(scRNA-seq)
from
three
additional
types
two
newly
generated
scRNA-seq
datasets
rare
namely
epithelial-myoepithelial
carcinoma
(EMC)
mucoepidermoid
(MEC),
expanded
our
understanding
CAF
heterogeneity.
Cell-cell
interaction
conducted
within
context
highlighted
pivotal
roles
matrix
(mCAFs)
angiogenesis
inflammatory
(iCAFs)
shaping
immunosuppressive
microenvironment.
In
patients
with
breast
(BRCA)
undergoing
anti-PD-1
immunotherapy,
iCAFs
demonstrated
heightened
capacity
facilitating
proliferation,
promoting
epithelial-mesenchymal
transition
(EMT),
contributing
to
establishment
an
Furthermore,
scoring
system
based
on
showed
significant
correlation
immune
therapy
response
melanoma
patients.
Lastly,
provided
web
interface
(
https://chenxisd.shinyapps.io/pancaf/
)
for
research
community
investigate
pan-cancer.
Science Translational Medicine,
Год журнала:
2023,
Номер
15(721)
Опубликована: Ноя. 8, 2023
Astrocytes
are
abundant
glial
cells
in
the
central
nervous
system
(CNS)
that
play
active
roles
health
and
disease.
Recent
technologies
have
uncovered
functional
heterogeneity
of
astrocytes
their
extensive
interactions
with
other
cell
types
CNS.
In
this
Review,
we
highlight
intricate
between
astrocytes,
CNS-resident
cells,
CNS-infiltrating
as
well
potential
therapeutic
value
context
inflammation
neurodegeneration.
Journal of genetics and genomics/Journal of Genetics and Genomics,
Год журнала:
2023,
Номер
50(9), С. 625 - 640
Опубликована: Март 27, 2023
The
ability
to
explore
life
kingdoms
is
largely
driven
by
innovations
and
breakthroughs
in
technology,
from
the
invention
of
microscope
350
years
ago
recent
emergence
single-cell
sequencing,
which
scientific
community
has
been
able
visualize
at
an
unprecedented
resolution.
Most
recently,
Spatially
Resolved
Transcriptomics
(SRT)
technologies
have
filled
gap
probing
spatial
or
even
three-dimensional
organization
molecular
foundation
behind
mysteries
life,
including
origin
different
cellular
populations
developed
totipotent
cells
human
diseases.
In
this
review,
we
introduce
progress
challenges
on
SRT
perspectives
bioinformatic
tools,
as
well
representative
applications.
With
currently
fast-moving
promising
results
early
adopted
research
projects,
can
foresee
bright
future
such
new
tools
understanding
most
profound
analytical
level.
Signal Transduction and Targeted Therapy,
Год журнала:
2023,
Номер
8(1)
Опубликована: Авг. 24, 2023
The
proper
transfer
of
genetic
information
from
DNA
to
RNA
protein
is
essential
for
cell-fate
control,
development,
and
health.
Methylation
DNA,
RNAs,
histones,
non-histone
proteins
a
reversible
post-synthesis
modification
that
finetunes
gene
expression
function
in
diverse
physiological
processes.
Aberrant
methylation
caused
by
mutations
or
environmental
stimuli
promotes
various
diseases
accelerates
aging,
necessitating
the
development
therapies
correct
disease-driver
imbalance.
In
this
Review,
we
summarize
operating
system
across
central
dogma,
which
includes
writers,
erasers,
readers,
reader-independent
outputs.
We
then
discuss
how
dysregulation
contributes
neurological
disorders,
cancer,
aging.
Current
small-molecule
compounds
target
modifiers
show
modest
success
certain
cancers.
methylome-wide
action
lack
specificity
lead
undesirable
biological
effects
cytotoxicity,
limiting
their
therapeutic
application,
especially
with
monogenic
cause
different
directions
changes.
Emerging
tools
capable
site-specific
manipulation
hold
great
promise
solve
dilemma.
With
refinement
delivery
vehicles,
these
new
are
well
positioned
advance
basic
research
clinical
translation
field.
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Ноя. 29, 2023
The
rapid
emergence
of
spatial
transcriptomics
(ST)
technologies
is
revolutionizing
our
understanding
tissue
architecture
and
biology.
Although
current
ST
methods,
whether
based
on
next-generation
sequencing
(seq-based
approaches)
or
fluorescence
in
situ
hybridization
(image-based
approaches),
offer
valuable
insights,
they
face
limitations
either
cellular
resolution
transcriptome-wide
profiling.
To
address
these
limitations,
we
present
SpatialScope,
a
unified
approach
integrating
scRNA-seq
reference
data
using
deep
generative
models.
With
innovation
model
algorithm
designs,
SpatialScope
not
only
enhances
seq-based
to
achieve
single-cell
resolution,
but
also
accurately
infers
expression
levels
for
image-based
data.
We
demonstrate
SpatialScope's
utility
through
simulation
studies
real
analysis
from
both
approaches.
provides
characterization
structures
at
facilitating
downstream
analysis,
including
detecting
communication
ligand-receptor
interactions,
localizing
subtypes,
identifying
spatially
differentially
expressed
genes.
Trends in Immunology,
Год журнала:
2023,
Номер
44(7), С. 499 - 511
Опубликована: Май 24, 2023
The
human
intestinal
microbiome
has
coevolved
with
its
host
to
establish
a
stable
homeostatic
relationship
hallmark
features
of
mutualistic
symbioses,
yet
the
mechanistic
underpinnings
host-microbiome
interactions
are
incompletely
understood.
Thus,
it
is
an
opportune
time
conceive
common
framework
for
microbiome-mediated
regulation
immune
function.
We
propose
term
conditioned
immunity
describe
multifaceted
mechanisms
by
which
modulates
immunity.
In
this
regard,
microbial
colonization
conditioning
exposure
that
durable
effects
on
function
through
action
secondary
metabolites,
foreign
molecular
patterns,
and
antigens.
Here,
we
discuss
how
spatial
niches
impact
products
at
level
dose
timing,
elicit
diverse
responses.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Дек. 8, 2023
Emerging
imaging
spatial
transcriptomics
(iST)
platforms
and
coupled
analytical
methods
can
recover
cell-to-cell
interactions,
groups
of
spatially
covarying
genes,
gene
signatures
associated
with
pathological
features,
are
thus
particularly
well-suited
for
applications
in
formalin
fixed
paraffin
embedded
(FFPE)
tissues.
Here,
we
benchmarked
the
performance
three
commercial
iST
on
serial
sections
from
tissue
microarrays
(TMAs)
containing
23
tumor
normal
types
both
relative
technical
biological
performance.
On
matched
found
that
10x
Xenium
shows
higher
transcript
counts
per
without
sacrificing
specificity,
but
all
concord
to
orthogonal
RNA-seq
datasets
perform
resolved
cell
typing,
albeit
different
false
discovery
rates,
segmentation
error
frequencies,
varying
degrees
sub-clustering
downstream
analyses.
Taken
together,
our
analyses
provide
a
comprehensive
benchmark
guide
choice
method
as
researchers
design
studies
precious
samples
this
rapidly
evolving
field.
