Frontiers in Cell and Developmental Biology,
Journal Year:
2023,
Volume and Issue:
11
Published: March 3, 2023
Spatial
transcriptome
technology
acquires
gene
expression
profiles
while
retaining
spatial
location
information,
it
displays
the
properties
of
cells
in
situ
.
Through
investigation
cell
heterogeneity,
microenvironment,
function,
and
cellular
interactions,
can
deeply
explore
pathogenic
mechanisms
cell-type-specific
responses
localization
neurological
diseases.
The
present
article
overviews
technologies
based
on
microdissection,
hybridization,
sequencing,
capture,
live
labeling.
Each
is
described
along
with
its
methods,
detection
throughput,
resolution,
benefits,
drawbacks.
Furthermore,
their
applications
neurodegenerative
disease,
neuropsychiatric
illness,
stroke
epilepsy
are
outlined.
This
information
be
used
to
understand
disease
mechanisms,
pick
therapeutic
targets,
establish
biomarkers.
Signal Transduction and Targeted Therapy,
Journal Year:
2023,
Volume and Issue:
8(1)
Published: Aug. 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.
Frontiers in Oncology,
Journal Year:
2022,
Volume and Issue:
12
Published: Oct. 13, 2022
In
recent
years,
spatial
transcriptomics
(ST)
technologies
have
developed
rapidly
and
been
widely
used
in
constructing
tissue
atlases
characterizing
spatiotemporal
heterogeneity
of
cancers.
Currently,
ST
has
to
profile
multiple
cancer
types.
Besides,
is
a
benefit
for
identifying
comprehensively
understanding
special
areas
such
as
tumor
interface
tertiary
lymphoid
structures
(TLSs),
which
exhibit
unique
microenvironments
(TMEs).
Therefore,
also
shown
great
potential
improve
pathological
diagnosis
identify
novel
prognostic
factors
cancer.
This
review
presents
advances
prospects
applications
on
research
based
well
the
challenges.
Advanced Science,
Journal Year:
2023,
Volume and Issue:
10(16)
Published: April 7, 2023
Spatial
transcriptomics
is
a
newly
emerging
field
that
enables
high-throughput
investigation
of
the
spatial
localization
transcripts
and
related
analyses
in
various
applications
for
biological
systems.
By
transitioning
from
conventional
studies
to
"in
situ"
biology,
can
provide
transcriptome-scale
information.
Currently,
ability
simultaneously
characterize
gene
expression
profiles
cells
relevant
cellular
environment
paradigm
shift
studies.
In
this
review,
recent
progress
its
neuroscience
cancer
are
highlighted.
Technical
aspects
existing
technologies
future
directions
new
developments
(as
March
2023),
computational
analysis
transcriptome
data,
application
notes
studies,
discussions
regarding
multi-omics
their
expanding
roles
biomedical
emphasized.
Computational and Structural Biotechnology Journal,
Journal Year:
2023,
Volume and Issue:
21, P. 940 - 955
Published: Jan. 1, 2023
Advances
in
transcriptomic
technologies
have
deepened
our
understanding
of
the
cellular
gene
expression
programs
multicellular
organisms
and
provided
a
theoretical
basis
for
disease
diagnosis
therapy.
However,
both
bulk
single-cell
RNA
sequencing
approaches
lose
spatial
context
cells
within
tissue
microenvironment,
development
transcriptomics
has
made
overall
bias-free
access
to
transcriptional
information
possible.
Here,
we
elaborate
help
researchers
select
best-suited
technology
their
goals
integrate
vast
amounts
data
facilitate
accessibility
availability.
Then,
marshal
various
computational
analyze
purposes
describe
multimodal
omics
its
potential
application
tumor
tissue.
Finally,
provide
detailed
discussion
outlook
technologies,
resources
analysis
guide
current
future
research
on
transcriptomics.
Nature Communications,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: Jan. 31, 2023
Abstract
Spatially
resolved
transcriptomics
has
enabled
precise
genome-wide
mRNA
expression
profiling
within
tissue
sections.
The
performance
of
methods
targeting
the
polyA
tails
relies
on
availability
specimens
with
high
RNA
quality.
Moreover,
cost
currently
available
spatial
assays
requires
a
careful
sample
screening
process
to
increase
chance
obtaining
high-quality
data.
Indeed,
upfront
analysis
quality
can
show
considerable
variability
due
handling,
storage,
and/or
intrinsic
factors.
We
present
RNA-Rescue
Spatial
Transcriptomics
(RRST),
workflow
designed
improve
recovery
from
fresh
frozen
moderate
low
First,
we
provide
benchmark
RRST
against
standard
Visium
gene
protocol
samples
represented
by
mouse
brain
and
prostate
cancer
samples.
Then,
test
sections
collected
five
challenging
types,
including
human
lung,
colon,
small
intestine,
pediatric
tumor,
bone/cartilage.
In
total,
analyze
52
demonstrate
that
is
versatile,
powerful,
reproducible
for
different
qualities
origins.
Nucleic Acids Research,
Journal Year:
2023,
Volume and Issue:
52(D1), P. D882 - D890
Published: Oct. 4, 2023
Abstract
The
development
of
spatial
transcriptome
sequencing
technology
has
revolutionized
our
comprehension
complex
tissues
and
propelled
life
health
sciences
into
an
era
omics.
However,
the
current
availability
databases
for
accessing
analyzing
transcriptomic
data
is
limited.
In
response,
we
have
established
CROST
(https://ngdc.cncb.ac.cn/crost),
a
comprehensive
repository
transcriptomics.
encompasses
high-quality
samples
houses
182
datasets
from
diverse
species,
organs,
diseases,
comprising
1033
sub-datasets
48
043
tumor-related
spatially
variable
genes
(SVGs).
Additionally,
it
standardized
processing
pipeline,
integrates
single-cell
RNA
deconvolution
transcriptomics
data,
evaluates
correlation,
colocalization,
intercellular
communication,
biological
function
annotation
analyses.
Moreover,
transcriptome,
epigenome,
genome
to
explore
tumor-associated
SVGs
provides
understanding
their
roles
in
cancer
progression
prognosis.
Furthermore,
two
online
tools,
single-sample
gene
set
enrichment
analysis
SpatialAP,
users
annotate
analyze
uploaded
data.
user-friendly
interface
facilitates
browsing,
searching,
analyzing,
visualizing,
downloading
desired
information.
Collectively,
offers
fresh
insights
tissue
structure
foundation
multiple
mechanisms
particularly
tumor
tissues.
Clinical and Translational Medicine,
Journal Year:
2023,
Volume and Issue:
13(12)
Published: Dec. 1, 2023
Abstract
Background
Cancer‐associated
fibroblasts
(CAFs)
are
potential
targets
for
cancer
therapy.
Due
to
the
heterogeneity
of
CAFs,
influence
CAF
subpopulations
on
progression
lung
is
still
unclear,
which
impedes
translational
advances
in
targeting
CAFs.
Methods
We
performed
single‐cell
RNA
sequencing
(scRNA‐seq)
tumour,
paired
tumour‐adjacent,
and
normal
samples
from
16
non‐small
cell
(NSCLC)
patients.
were
analyzed
after
integration
with
published
NSCLC
scRNA‐seq
data.
SpaTial
enhanced
resolution
omics‐sequencing
(Stereo‐seq)
was
applied
tumour
tumour‐adjacent
seven
patients
map
architecture
major
populations
microenvironment
(TME).
Immunohistochemistry
(IHC)
multiplexed
IHC
(mIHC)
used
validate
marker
gene
expression
association
CAFs
immune
infiltration
TME.
Results
A
subcluster
myofibroblastic
POSTN
+
significantly
enriched
advanced
tumours
presented
signatures
related
extracellular
matrix
remodeling,
invasion
pathways
suppression.
Stereo‐seq
mIHC
demonstrated
that
close
localization
SPP1
macrophages
associated
exhausted
phenotype
lower
T
cells.
or
abundance
poor
prognosis
NSCLC.
Conclusions
Our
study
identified
a
subpopulation,
might
associate
promote
formation
desmoplastic
participate
Furthermore,
we
showed
clinical
outcomes
may
provide
new
insights
treatment
iScience,
Journal Year:
2023,
Volume and Issue:
26(4), P. 106359 - 106359
Published: March 9, 2023
As
modern
biological
sciences
evolve
from
investigation
of
individual
molecules
and
pathways
to
growing
emphasis
on
global
systems-based
processes,
increasing
efforts
have
focused
combining
the
study
genomics
with
that
other
omics
technologies,
including
epigenomics,
transcriptomics,
quantitative
proteomics,
analyses
post-translational
modifications
(PTMs)
metabolomics,
characterize
specific
or
pathological
processes.
In
addition,
emerging
genome-wide
functional
screening
technologies
further
help
researchers
identify
key
regulators
immune
functions.
Derived
these
multi-omics
single
cell
sequencing
analysis
multiple
layers
offers
an
overview
intra-tissue
intra-organ
heterogeneity.
this
review,
we
summarize
advances
in
tools
explore
functions
applications
approaches
clinical
disorders,
aiming
provide
outlook
potential
opportunities
challenges
pose
future
field
immunology.
