Single-cell RNA-sequencing and genome-wide Mendelian randomisation along with abundant machine learning methods identify a novel B cells signature in gastric cancer
Discover Oncology,
Год журнала:
2025,
Номер
16(1)
Опубликована: Янв. 6, 2025
Gastric
cancer
(GC)
has
a
poor
prognosis,
considerable
cellular
heterogeneity,
and
ranks
fifth
among
malignant
tumours.
Understanding
the
tumour
microenvironment
(TME)
intra-tumor
heterogeneity
(ITH)
may
lead
to
development
of
novel
GC
treatments.
The
single-cell
RNA
sequencing
(scRNA-seq)
dataset
was
obtained
from
Gene
Expression
Omnibus
(GEO)
database,
where
diverse
immune
cells
were
isolated
re-annotated
based
on
cell
markers
established
in
original
study
ascertain
their
individual
characteristics.
We
conducted
weighted
gene
co-expression
network
analysis
(WGCNA)
identify
genes
with
significant
correlation
GC.
Utilising
bulk
data,
we
employed
machine
learning
integration
methods
train
specific
biomarkers
for
diagnostic
combinations.
A
two-sample
Mendelian
randomisation
performed
investigate
causal
effect
gastric
(GC).
Ultimately,
utilised
DSigDB
database
acquire
associations
between
signature
pharmaceuticals.
18
that
made
up
as
follows:
ZFAND2A,
PBX4,
RAMP2,
NNMT,
RNASE1,
CD93,
CDH5,
NFKBIE,
VWF,
DAB2,
FAAH2,
VAT1,
MRAS,
TSPAN4,
EPAS1,
AFAP1L1,
DNM3.
Patients
categorised
into
high-risk
low-risk
groups
according
risk
scores.
Individuals
cohort
exhibited
dismal
outlook.
demonstrated
individuals
genetic
predisposition
elevated
NFKBIE
levels
heightened
likelihood
acquiring
Molecular
docking
indicates
gemcitabine
chloropyramine
serve
effective
therapeutics
against
NFKBIE.
developed
validated
utilising
scRNA-seq
data
patients.
function
biomarker
therapeutic
target
Язык: Английский
Construction of a TAN-associated risk score model with integrated multi-omics data analysis and clinical validation in gastric cancer
Life Sciences,
Год журнала:
2024,
Номер
349, С. 122731 - 122731
Опубликована: Май 21, 2024
Язык: Английский
A prognostic model based on CLEC6A predicts clinical outcome of breast cancer patients
International Immunopharmacology,
Год журнала:
2024,
Номер
137, С. 112411 - 112411
Опубликована: Июнь 12, 2024
Язык: Английский
A novel platelets-related gene signature for predicting prognosis, immune features and drug sensitivity in gastric cancer
Frontiers in Immunology,
Год журнала:
2024,
Номер
15
Опубликована: Ноя. 13, 2024
Background
Platelets
can
dynamically
regulate
tumor
development
and
progression.
Nevertheless,
research
on
the
predictive
value
specific
roles
of
platelets
in
gastric
cancer
(GC)
is
limited.
This
aims
to
establish
a
platelets-related
gene
signature
GC
with
prognostic
therapeutic
implications.
Methods
We
downloaded
transcriptome
data
clinical
materials
patients
(n=378)
from
The
Cancer
Genome
Atlas
(TCGA)
database.
Prognostic
genes
screened
by
univariate
Cox
regression
were
included
Least
Absolute
Shrinkage
Selection
Operator
(LASSO)
analysis
construct
risk
model.
Kaplan-Meier
curves
receiver
operating
characteristic
(ROCs)
performed
TCGA
cohort
three
independent
validation
cohorts.
A
nomogram
integrating
score
clinicopathological
features
was
constructed.
Functional
enrichment
microenvironment
(TME)
analyses
performed.
Drug
sensitivity
prediction
conducted
through
Therapeutics
Response
Portal
(CTRP)
Finally,
expression
ten
validated
quantitative
real-time
PCR
(qRT-PCR).
Results
ten-gene
(
SERPINE1
,
ANXA5
DGKQ
PTPN6
F5
DGKB
PCDH7
GNG11
APOA1
TF
)
model
finally
Patients
categorized
as
high-
or
low-risk
using
median
threshold.
area
under
ROC
curve
(AUC)
values
for
1-,
2-,
3-year
overall
survival
(OS)
training
0.670,
0.695,
0.707,
respectively.
Survival
showed
better
OS
AUCs
predicting
0.708,
0.763,
0.742,
TME
revealed
higher
M2
macrophage
infiltration
an
immunosuppressive
high-risk
group.
Furthermore,
High-risk
tended
be
more
sensitive
thalidomide,
MK-0752,
BRD-K17060750.
Conclusion
novel
we
identified
could
used
prognosis
treatment
GC.
Язык: Английский
Prognostic impact and immunotherapeutic implications of NETosis-related prognostic model in clear cell renal cell carcinoma
Xingjun Mao,
Wen Huang,
Qing Xue
и другие.
Research Square (Research Square),
Год журнала:
2024,
Номер
unknown
Опубликована: Март 15, 2024
Abstract
Background
The
ramifications
of
necroptosis
on
the
prognostication
clear
cell
renal
carcinoma
(ccRCC)
remain
inadequately
expounded.
Methods
A
prognostic
model
delineating
facets
in
ccRCC
was
constructed,
employing
a
compendium
algorithms.
External
validation
effectuated
using
E-MTAB-1980
dataset.
exploration
immune
infiltration
scores
undertaken
through
exploitation
multiple
Single-gene
RNA
sequencing
data
were
procured
from
GSE171306
Real-time
quantitative
PCR
(RT-qPCR)
engaged
to
scrutinize
differential
expression
SLC25A37
across
cancer
and
paracancer
tissues,
as
well
diverse
lines.
Assessments
proliferative
metastatic
alterations
769-P
786-O
cells
accomplished
Cell
Counting
Kit-8
(CCK8)
wound
healing
assays.
Results
necroptosis-related
signature
(NRS)
emerges
discerning
metric,
patients'
attributes,
tumor
mutation
burden,
immunotherapy
response,
drug
susceptibility.
analysis
unveils
marked
enrichment
cells.
Concurrently,
RT-qPCR
discloses
overexpression
both
tissues
knockdown
mitigates
propensities
cells,
evidenced
by
CCK8
Conclusion
NRS
assumes
pivotal
role
ascertaining
prognosis,
susceptibility,
features
patients.
putative
player
immunosuppressive
microenvironments,
thereby
providing
prospective
avenue
for
design
innovative
immunotherapeutic
targets
ccRCC.
Язык: Английский
Prognostic impact and immunotherapeutic implications of NETosis-related prognostic model in clear cell renal cell carcinoma
Xingjun Mao,
Wen Huang,
Qing Xue
и другие.
Journal of Cancer Research and Clinical Oncology,
Год журнала:
2024,
Номер
150(5)
Опубликована: Май 27, 2024
Abstract
Background
The
ramifications
of
necroptosis
on
the
prognostication
clear
cell
renal
carcinoma
(ccRCC)
remain
inadequately
expounded.
Methods
A
prognostic
model
delineating
facets
in
ccRCC
was
constructed,
employing
a
compendium
algorithms.
External
validation
effectuated
using
E-MTAB-1980
dataset.
exploration
immune
infiltration
scores
undertaken
through
exploitation
multiple
Single-cell
RNA
sequencing
data
were
procured
from
GSE171306
Real-time
quantitative
PCR
(RT-qPCR)
engaged
to
scrutinize
differential
expression
SLC25A37
across
cancer
and
paracancer
tissues,
as
well
diverse
lines.
Assessments
proliferative
metastatic
alterations
769-P
786-O
cells
accomplished
Cell
Counting
Kit-8
(CCK8)
wound
healing
assays.
Results
necroptosis-related
signature
(NRS)
emerges
discerning
metric,
patients’
attributes,
tumor
mutation
burden,
immunotherapy
response,
drug
susceptibility.
analysis
unveils
marked
enrichment
cells.
Concurrently,
RT-qPCR
discloses
overexpression
both
tissues
knockdown
mitigates
propensities
cells,
evidenced
by
CCK8
Conclusion
NRS
assumes
pivotal
role
ascertaining
prognosis,
susceptibility,
features
patients.
putative
player
immunosuppressive
microenvironments,
thereby
providing
prospective
avenue
for
design
innovative
immunotherapeutic
targets
ccRCC.
Язык: Английский
TRIM8 as a predictor for prognosis in childhood acute lymphoblastic leukemia based on a signature of neutrophil extracellular traps
Waihin Tin,
Cuilan Xiao,
Kexin Sun
и другие.
Frontiers in Oncology,
Год журнала:
2024,
Номер
14
Опубликована: Авг. 19, 2024
Background
Neutrophil
extracellular
traps
(NETs)
can
be
attributed
to
the
metastasis,
occurrence,
and
immune
evasion
of
cancer
cells.
We
investigated
prognostic
value
NET-related
genes
in
childhood
acute
lymphoblastic
leukemia
(cALL)
patients.
Methods
Differential
gene
expression
analysis
was
conducted
on
samples
collected
from
public
databases.
Grouping
them
based
level
genes,
we
assessed
correlation
between
cell
types
risk
score
for
having
a
poor
prognosis
cALL,
with
an
evaluation
sensitivity
drugs
used
cALL.
further
divided
groups,
integrating
survival
data.
Subsequently,
methods
including
multivariable
Cox
algorithms,
least
absolute
shrinkage
selection
operator
(LASSO),
univariable
were
utilized
create
model
predicting
prognosis.
Experiments
lines
animals
performed
explore
functions
TRIM8,
selected
by
model.
To
validate
role
TRIM8
development,
lentivirus-mediated
overexpression
or
knockdown
employed
mice
T-ALL
B-ALL.
Results
Kaplan–Meier
(KM)
underscored
importance
differentially
expressed
identified
groups
participated
NETs,
enrichment
showing
mechanism.
Correlation
revealed
significant
associations
B
cells,
NK
mast
T
plasma
dendritic
monocytes.
The
IC
50
values
such
as
all-trans-retinoic
acid
(ATRA),
axitinib,
doxorubicin,
methotrexate,
sorafenib,
vinblastine
increased,
while
dasatinib
exhibited
lower
.
A
total
13
constructing
In
training,
testing,
merged
cohorts,
KM
demonstrated
significantly
improved
low-risk
cALL
patients
compared
high-risk
(
p
<
0.001).
area
under
curve
(AUC)
indicated
strong
predictive
performance.
Jurkat
SUP-B15
that
decreased
proliferation
lines.
Further
experiments
more
favorable
TRIM8-knockdown
showed
better
outcomes
when
knocked
down.
Conclusion
novelty
could
aid
development
personalized
treatments
Furthermore,
it
is
contributing
factor
cells
worsens
Язык: Английский