Clinical and Translational Medicine,
Год журнала:
2024,
Номер
14(3)
Опубликована: Март 1, 2024
Abstract
As
single‐cell
RNA
sequencing
enables
the
detailed
clustering
of
T‐cell
subpopulations
and
facilitates
analysis
metabolic
states
metabolite
dynamics,
it
has
gained
prominence
as
preferred
tool
for
understanding
heterogeneous
cellular
metabolism.
Furthermore,
synergistic
or
inhibitory
effects
various
pathways
within
T
cells
in
tumour
microenvironment
are
coordinated,
increased
activity
specific
generally
corresponds
to
functional
activity,
leading
diverse
behaviours
related
immune
cells,
which
shows
potential
tumour‐specific
induce
persistent
responses.
A
holistic
how
heterogeneity
governs
function
subsets
is
key
obtaining
field‐level
insights
into
immunometabolism.
Therefore,
exploring
mechanisms
underlying
interplay
between
metabolism
functions
will
pave
way
precise
immunotherapy
approaches
future,
empower
us
explore
new
methods
combating
tumours
with
enhanced
efficacy.
Scientific Reports,
Год журнала:
2024,
Номер
14(1)
Опубликована: Апрель 1, 2024
Abstract
Natural
killer
(NK)
cells
play
essential
roles
in
the
tumor
development,
diagnosis,
and
prognosis
of
tumors.
In
this
study,
we
aimed
to
establish
a
reliable
signature
based
on
marker
genes
NK
cells,
thus
providing
new
perspective
for
assessing
immunotherapy
patients
with
gastric
cancer
(GC).
We
analyzed
total
1560
samples
retrieved
from
public
database.
performed
comprehensive
analysis
single-cell
RNA-sequencing
(scRNA-seq)
data
identified
377
cells.
By
performing
Cox
regression
analysis,
established
12-gene
cell-associated
(NKCAS)
Cancer
Genome
Atlas
(TCGA)
cohort,
that
assigned
GC
into
low-risk
group
(LRG)
or
high-risk
(HRG).
TCGA
areas
under
curve
(AUC)
value
were
0.73,
0.81,
0.80
at
1,
3,
5
years.
External
validation
predictive
ability
was
then
validated
Gene
Expression
Omnibus
(GEO)
cohorts
(GSE84437).
The
expression
levels
measured
cell
lines
by
real-time
PCR.
Moreover,
NKCAS
as
an
independent
prognostic
factor
multivariate
analysis.
combined
variety
clinicopathological
characteristics
(age,
M
stage,
grade)
construct
nomogram
predict
survival
outcomes
patients.
LRG
showed
higher
immune
infiltration,
especially
CD8+
T
risk
score
negatively
associated
inflammatory
activities.
Importantly,
cohort
had
better
response
when
compared
HRG.
identification
study
suggests
potential
therapeutic
targets.
Additionally,
developed
signatures
nomograms
may
aid
clinical
management
GC.
Functional & Integrative Genomics,
Год журнала:
2025,
Номер
25(1)
Опубликована: Янв. 23, 2025
T
cells
are
involved
in
every
stage
of
tumor
development
and
significantly
influence
the
microenvironment
(TME).
Our
objective
was
to
assess
T-cell
marker
gene
expression
profiles,
develop
a
predictive
risk
model
for
human
papilloma
virus
(HPV)-negative
oral
squamous
cell
carcinoma
(OSCC)
utilizing
these
genes,
examine
correlation
between
score
immunotherapy
response.
We
acquired
scRNA-seq
data
HPV-negative
OSCC
from
GEO
datasets.
performed
cell‒cell
communication,
trajectory,
pathway
enrichment
analyses
T-cell-associated
genes.
In
addition,
we
constructed
validated
prognostic
patients
using
TCGA
assessed
immune
infiltration
status
.qRT-PCR
used
detect
level
prognosis-related
genes
different
groups.
ScRNA-seq
conducted
on
28,000
derived
14
samples
6
normal
samples.
identified
4,635
774
differentially
expressed
genes(DEGs)
associated
with
across
five
distinct
subtypes.
Through
integration
bulk-RNAseq
data,
established
based
DEGs
related
cells.
By
separating
into
high-risk
low-risk
groups
according
can
accurately
predict
their
survival
rates
TME.qRT-PCR
results
showed
that
compared
low
group,
PMEPA1,
SH2D2A,
SMS
PRDX4
were
up-regulated
high
group.
This
study
provides
resource
understanding
heterogeneity
models.
It
new
insights
predicting
OSCC.
Epithelial
cells
are
associated
with
tumor
immunity
through
interstitial
transformation,
yet
the
role
of
epithelial
immune‑related
genes
(EIGs)
in
this
process
remains
unclear.
Comprehending
mechanisms
behind
EIGs
within
lung
squamous
cell
carcinoma
(LUSC)
may
offer
an
explanation
to
these
issues.
The
present
study
aimed
explore
biological
patients
LUSC.
Based
on
data
from
Gene
Expression
Omnibus
and
Cancer
Genome
Atlas
databases,
a
survival
model
nomogram
was
established.
This
were
used
mechanism
LUSC
its
medical
significance
by
enrichment
analysis,
microenvironment,
immune
infiltration
function
correlation
analysis.
Finally,
reverse
transcription‑quantitative
PCR
(RT‑qPCR)
external
dataset
assess
expression
EIGs.
develop
4
as
predictors
for
patient
outcomes.
Survival
curves
revealed
that
higher
risk
had
more
negative
developed
based
entirely
accurate
prognosis
predictive
analysis
indicated
pathways
related
antigen
processing
presentation,
well
Epstein‑Barr
virus
infection,
prevalent
high‑risk
populations.
research
demonstrated
notable
rise
activated
dendritic
neutrophils
group.
Furthermore,
results
populations
particularly
susceptible
effects
afureserpine,
gefitinib
savolitinib.
outcomes
RT‑qPCR
consistent
those
bioinformatics
In
conclusion,
evaluation
effective
forecasting
guiding
drug
selection
A
worse
high
be
certain
viral
infections
presentation.
Tumor-associated
macrophages
(TAMs)
play
pivotal
roles
in
innate
immunity
and
contribute
to
the
advancement
of
lung
cancer.
We
aimed
identify
novel
TAM-related
biomarkers
significance
macrophage
infiltration
adenocarcinoma
(LUAD)
through
an
integrative
analysis
single-cell
RNA-sequencing
(scRNA-seq)
data.
To
describe
cell
atlas
construct
a
prognostic
signature
LUAD.
The
gene
linked
TAMs
was
identified
utilizing
Scanpy
from
scRNA-seq
dataset
GSE131907.
Subsequent
involved
evaluating
expression
levels
these
genes,
their
potential
molecular
mechanisms,
LUAD
using
data
Cancer
Genome
Atlas
(TCGA)
Gene
Expression
Omnibus
(GEO)
databases.
also
constructed
risk
score
models
LASSO
Cox
regression
for
genes.
underlying
mechanism
further
elucidated
application
GSEA,
ESTIMATE,
TIDE,
other
bioinformatic
algorithms.
Single-cell
described
by
analyze
29
samples
19
patients.
TAMs-related
(TGS)
as
independent
factor
differential
genes
(DEGs)
derived
pro-
anti-inflammatory
cells.
Risk
model
including
nine
(FOSL1,
ZNF697,
ADM,
UBE2S,
TICAM1,
S100P,
BIRC3,
TLE1,
DEFB1)
were
obtained
prognosis
construction.
Moreover,
underwent
additional
validation
four
external
GEO
cohorts:
GSE31210,
GSE72094,
GSE26939,
GSE30219.
Interestingly,
TGS-high
tumors
revealed
enrichments
TGF-β
signaling
hypoxia
pathways,
which
shown
low
immune
immunosuppression
ESTIMATE
TIDE
algorithm.
group
exhibited
lower
richness
diversity
T-cell
receptor
(TCR)
repertoire.
This
study
introduces
TGS
developed
analysis,
DEGs
High
enrichment
suggesting
utility
predicting
responses
patients
with
These
results
offer
promising
implications
development
therapeutic
strategies
Research Square (Research Square),
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 25, 2025
Efforts
to
understand
the
tumor
microenvironment
(TME)
through
basic
science
research
and
The
Cancer
Genome
Atlas
(TCGA)
data
analysis
have
led
creation
of
unique
immune
transcriptomic
signatures
from
tumor-infiltrating
lymphocytes
(TIL).
However,
no
pan-cancer
has
been
conducted
compare
prognostic
performance
these
using
overall
survival
(OS)
or
progression-free
interval
(PFI)
as
endpoints.
We
compiled
a
library
146
TIL-immune
evaluated
gene
signature
score
correlation
with
OS
PFI
for
9,961
available
TCGA
samples
across
33
cancer
types.
Zhang
CD8
TCS
demonstrated
higher
accuracy
in
prognosticating
both
landscape,
however,
variability
was
seen
types
germ
cell
origin.
Cluster
group
six
(Oh.Cd8.MAIT,
Grog.8KLRB1,
Oh.TIL_CD4.GZMK,
Grog.CD4.TCF7,
Oh.CD8.RPL,
Grog.CD4.RPL32)
whose
association
could
potentially
be
conserved
multiple
International Journal of Molecular Sciences,
Год журнала:
2023,
Номер
24(3), С. 3042 - 3042
Опубликована: Фев. 3, 2023
Radioresistance
is
a
major
obstacle
for
the
successful
therapy
of
many
cancers,
including
non-small
cell
lung
cancer
(NSCLC).
To
elucidate
mechanism
radioresistance
NSCLC
cells
and
to
identify
key
molecules
conferring
radioresistance,
radioresistant
subclones
p53
wild-type
A549
p53-deficient
H1299
cultures
were
established.
The
transcriptional
changes
between
parental
investigated
by
RNA-seq.
In
total,
expression
levels
36,596
genes
measured.
Changes
in
activation
intracellular
molecular
pathways
surviving
irradiation
relative
quantified
using
Oncobox
bioinformatics
platform.
Following
30
rounds
2
Gy
irradiation,
total
322
differentially
expressed
A549IR
cells.
For
(H1299)
cells,
irradiated
populations
differed
1628
1616
pathways.
associated
with
reflects
complex
biological
processes
involved
clinical
eradication
might
serve
as
potential
biomarker
therapeutic
target
treatment.
Current Proteomics,
Год журнала:
2023,
Номер
20(3), С. 208 - 221
Опубликована: Июнь 1, 2023
Background:
Recent
studies
have
validated
the
role
of
Pericentriolar
Material
1
(PCM1)
in
several
malignant
tumour
cell
lines,
but
its
specific
biological
function
lung
adenocarcinoma
(LUAD)
remains
unclear.
Objective:
To
address
this
gap,
study
analyzed
411
LUAD
and
control
samples
to
evaluate
prognostic
value
PCM1
using
Cox
regression
analysis.
Methods:
Multiple
genes
co-expressed
with
were
also
investigate
processes
roles
involved
PCM1.
An
endogenous
competitive
network
as
key
gene
was
constructed
uncover
regulatory
relationships
LUAD.
The
further
explored
immunological
characteristics
different
expression
groups
based
on
immune
infiltration
Results:
These
findings
indicated
that
higher
levels
associated
better
survival
prognoses,
possibly
due
antagonistic
effects
RHOC.
Immunological
analysis
revealed
a
significant
correlation
between
various
levels,
including
CD4+
T
cells,
naïve
B
M2
macrophages,
mast
cells.
However,
there
no
relationship
MSI,
TMB,
or
stemness,
although
it
positively
correlated
m6A
genes.
Patients
lower
responded
CTLA-4
therapy.
estimated
some
chemotherapeutic
targeted
agents
might
be
effective
treating
patients
high
levels.
mainly
expressed
cytoplasmic
membranous
structures.
Conclusion:
shows
potential
biomarker
for
strong
ability
enhance
anticancer
treatment
sensitivity.
