Seminars in Immunopathology,
Journal Year:
2022,
Volume and Issue:
45(1), P. 145 - 157
Published: Nov. 21, 2022
Abstract
Multiplexed
imaging,
which
enables
spatial
localization
of
proteins
and
RNA
to
cells
within
tissues,
complements
existing
multi-omic
technologies
has
deepened
our
understanding
health
disease.
CODEX,
a
multiplexed
single-cell
imaging
technology,
utilizes
microfluidics
system
that
incorporates
DNA
barcoded
antibodies
visualize
50
+
cellular
markers
at
the
level.
Here,
we
discuss
latest
applications
CODEX
studies
cancer,
autoimmunity,
infection
as
well
current
bioinformatics
approaches
for
analysis
data
from
preprocessing
cell
segmentation
marker
quantification
techniques.
We
conclude
with
commentary
on
challenges
future
developments
profiling.
Signal Transduction and Targeted Therapy,
Journal Year:
2022,
Volume and Issue:
7(1)
Published: April 1, 2022
Abstract
The
combination
of
spatial
transcriptomics
(ST)
and
single
cell
RNA
sequencing
(scRNA-seq)
acts
as
a
pivotal
component
to
bridge
the
pathological
phenomes
human
tissues
with
molecular
alterations,
defining
in
situ
intercellular
communications
knowledge
on
spatiotemporal
medicine.
present
article
overviews
development
ST
aims
evaluate
clinical
translational
values
for
understanding
pathogenesis
uncovering
disease-specific
biomarkers.
We
compare
advantages
disadvantages
sequencing-
imaging-based
technologies
highlight
opportunities
challenges
ST.
also
describe
bioinformatics
tools
necessary
dissecting
patterns
gene
expression
cellular
interactions
potential
applications
diseases
practice
one
important
issues
medicine,
including
neurology,
embryo
development,
oncology,
inflammation.
Thus,
clear
objectives,
designs,
optimizations
sampling
procedure
protocol,
repeatability
ST,
well
simplifications
analysis
interpretation
are
key
translate
from
bench
clinic.
Frontiers in Endocrinology,
Journal Year:
2023,
Volume and Issue:
14
Published: April 19, 2023
Background
Bladder
cancer
(BLCA)
is
the
most
common
malignancy
of
urinary
tract.
On
other
hand,
disulfidptosis,
a
mechanism
disulfide
stress-induced
cell
death,
closely
associated
with
tumorigenesis
and
progression.
Here,
we
investigated
impact
disulfidptosis-related
genes
(DRGs)
on
prognosis
BLCA,
identified
various
DRG
clusters,
developed
risk
model
to
assess
patient
prognosis,
immunological
profile,
treatment
response.
Methods
The
expression
mutational
characteristics
four
DRGs
were
first
analyzed
in
bulk
RNA-Seq
single-cell
RNA
sequencing
data,
IHC
staining
role
BLCA
progression,
two
clusters
by
consensus
clustering.
Using
differentially
expressed
(DEGs)
from
these
transformed
ten
machine
learning
algorithms
into
more
than
80
combinations
finally
selected
best
algorithm
construct
prognostic
signature
(DRPS).
We
based
this
selection
mean
C-index
three
cohorts.
Furthermore,
explored
differences
clinical
characteristics,
landscape,
immune
infiltration,
predicted
efficacy
immunotherapy
between
high
low-risk
groups.
To
visually
depict
value
DRPS,
employed
nomograms.
Additionally,
verified
whether
DRPS
predicts
response
patients
utilizing
Tumour
Immune
Dysfunction
Rejection
(TIDE)
IMvigor
210
Results
In
integrated
cohort,
several
gene
that
differed
significantly
overall
survival
(OS)
tumor
microenvironment.
After
integration
clinicopathological
features,
showed
robust
predictive
power.
Based
median
score
divided
(LR)
high-risk
(HR)
groups,
LR
group
having
better
higher
load
being
sensitive
chemotherapy.
Conclusion
Our
study,
therefore,
provides
valuable
tool
further
guide
management
tailor
patients,
offering
new
insights
individualized
treatment.
Genomics,
Journal Year:
2023,
Volume and Issue:
115(5), P. 110671 - 110671
Published: June 21, 2023
The
diverse
cell
types
of
an
organ
have
a
highly
structured
organization
to
enable
their
efficient
and
correct
function.
To
fully
appreciate
gene
functions
in
given
type,
one
needs
understand
how
much,
when
where
the
is
expressed.
Classic
bulk
RNA
sequencing
popular
single
destroy
structural
fail
provide
spatial
information.
However,
location
expression
or
complex
tissue
provides
key
clues
comprehend
neighboring
genes
cells
cross
talk,
transduce
signals
work
together
as
team
complete
job.
functional
requirement
for
content
has
been
driving
force
rapid
development
transcriptomics
technologies
past
few
years.
Here,
we
present
overview
current
with
special
focus
on
commercially
available
currently
being
commercialized
technologies,
highlight
applications
by
category
discuss
experimental
considerations
first
experiment.
Journal of Biomedical Science,
Journal Year:
2022,
Volume and Issue:
29(1)
Published: Nov. 14, 2022
Abstract
In
the
past
decade,
single-cell
technologies
have
revealed
heterogeneity
of
tumor-immune
microenvironment
at
genomic,
transcriptomic,
and
proteomic
levels
furthered
our
understanding
mechanisms
tumor
development.
Single-cell
also
been
used
to
identify
potential
biomarkers.
However,
spatial
information
about
such
as
cell
locations
cell–cell
interactomes
is
lost
in
these
approaches.
Recently,
multi-omics
study
transcriptomes,
proteomes,
metabolomes
microenvironments
several
types
cancer,
data
obtained
from
methods
has
combined
with
immunohistochemistry
multiparameter
analysis
yield
markers
cancer
progression.
Here,
we
review
numerous
cutting-edge
‘omics
techniques,
their
application
microenvironment,
remaining
technical
challenges.
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.
Biomolecules,
Journal Year:
2023,
Volume and Issue:
13(1), P. 156 - 156
Published: Jan. 12, 2023
Development
from
single
cells
to
multicellular
tissues
and
organs
involves
more
than
just
the
exact
replication
of
cells,
which
is
known
as
differentiation.
The
primary
focus
research
into
mechanism
differentiation
has
been
differences
in
gene
expression
profiles
between
individual
cells.
However,
it
predominantly
conducted
at
low
throughput
bulk
levels,
challenging
efforts
understand
molecular
mechanisms
during
developmental
process
animals
humans.
During
last
decades,
rapid
methodological
advancements
genomics
facilitated
ability
study
processes
a
genome-wide
level
finer
resolution.
Particularly,
sequencing
transcriptomes
single-cell
resolution,
enabled
by
RNA-sequencing
(scRNA-seq),
was
breath-taking
innovation,
allowing
scientists
gain
better
understanding
cell
lineage
process.
isolation
scRNA-seq
results
loss
spatial
information
consequently
limits
our
specific
functions
performed
different
regions
or
organs.
This
greatly
encourages
emergence
transcriptomic
discipline
tools.
Here,
we
summarize
recent
application
tools
for
biology.
We
also
discuss
limitations
current
approaches,
well
possible
solutions
future
prospects.
