Identification of Novel Biomarkers for Ischemic Stroke Through Integrated Bioinformatics Analysis and Machine Learning
Journal of Molecular Neuroscience,
Год журнала:
2025,
Номер
75(1)
Опубликована: Янв. 25, 2025
Язык: Английский
Identification of Cardiometabolic Protein Biomarkers for Acute Myocardial Infarction Using Olink Proteomics
Journal of Inflammation Research,
Год журнала:
2025,
Номер
Volume 18, С. 2629 - 2646
Опубликована: Фев. 1, 2025
Acute
myocardial
infarction
(AMI)
is
a
critical
cardiovascular
event
characterized
by
sudden
coronary
blood
flow
interruption,
leading
to
ischemia
and
necrosis.
Despite
advances
in
acute
therapeutic
measures,
understanding
the
metabolic
damage
related
AMI,
particularly
through
specific
protein
expressions,
remains
limited.
This
study
utilized
Olink
metabolomics
technology
explore
metabolism-related
biomarkers
associated
with
aiming
address
clinical
need
for
early
diagnosis
targeted
therapy.
analyze
92
proteins
samples
from
20
AMI
patients
10
healthy
controls.
Differentially
expressed
were
identified
using
statistical
t-tests,
followed
functional
enrichment
analysis
(GO
KEGG)
protein-protein
interaction
network
construction.
Five
core
validated
plasma
an
additional
125
120
controls
via
enzyme-linked
immunosorbent
assay.
To
evaluate
diagnostic
performance,
receiver
operating
characteristic
curves
generated
GEO-related
datasets,
Mendelian
randomization
was
employed
investigate
causal
relationship
between
risk.
The
32
significantly
altered
expression
levels
Among
these,
five
proteins-PCOLCE,
FCN2,
REG1A,
DEFA1,
CRTAC1-were
key
biological
processes
such
as
metabolism,
collagen
formation,
PI3K/AKT
signaling
pathway.
These
showed
strong
correlations
indicators,
including
BMI,
LVEF,
NT-proBNP,
CK-MB,
cTnT.
FCN2
DEFA1
further
having
risk,
indicating
their
potential
biomarkers.
PCOLCE,
CRTAC1
are
risk
assessment
of
AMI.
findings
suggest
that
these
could
serve
targets
future
interventions
aimed
at
mitigating
Язык: Английский
Olink Profiling of Intestinal Tissue Identifies Novel Biomarkers For Colorectal Cancer
Journal of Proteome Research,
Год журнала:
2025,
Номер
24(2), С. 599 - 611
Опубликована: Янв. 6, 2025
Comprehensive
protein
profiling
in
intestinal
tissues
provides
detailed
information
about
the
pathogenesis
of
colorectal
cancer
(CRC).
This
study
quantified
expression
levels
92
oncology-related
proteins
tumors,
paired
para-carcinoma
tissues,
and
remote
normal
from
a
cohort
52
CRC
patients
utilizing
Olink
technology.
The
proteomic
profile
closely
resembled
that
while
distinctly
differing
tumors.
Among
68
differentially
expressed
(DEPs)
identified
between
tumor
WISP-1,
ESM-1,
TFPI-2
showed
most
pronounced
alterations
exhibited
relatively
strong
correlations.
These
markers
also
presented
highest
AUC
values
for
distinguishing
tissue
types.
Bioinformatic
analysis
DEPs
revealed
plasma
membrane
PI3K-AKT
signaling
pathway
were
among
enriched
GO
terms
KEGG
pathways.
Furthermore,
although
is
typically
recognized
as
suppressor,
both
enzyme
linked
immunosorbent
assay
(ELISA)
analyses
have
demonstrated
its
significantly
elevated
tumors
compared
with
tissues.
To
best
our
knowledge,
this
first
to
proteome
using
work
offers
valuable
insights
into
potential
biomarkers
therapeutic
targets
CRC,
complementing
circulating
proteins.
Язык: Английский
Large-Scale Proteomics Improve Prediction of Chronic Kidney Disease in People With Diabetes
Diabetes Care,
Год журнала:
2024,
Номер
47(10), С. 1757 - 1763
Опубликована: Июль 23, 2024
OBJECTIVE
To
develop
and
validate
a
protein
risk
score
for
predicting
chronic
kidney
disease
(CKD)
in
patients
with
diabetes
compare
its
predictive
performance
validated
clinical
model
(CKD
Prediction
Consortium
[CKD-PC])
CKD
polygenic
score.
RESEARCH
DESIGN
AND
METHODS
This
cohort
study
included
2,094
who
had
proteomics
genetic
information
no
history
of
at
baseline
from
the
UK
Biobank
Pharma
Proteomics
Project.
Based
on
nearly
3,000
plasma
proteins,
including
11
proteins
was
constructed
training
set
(including
1,047
participants;
117
events).
RESULTS
The
median
follow-up
duration
12.1
years.
In
test
112
events),
positively
associated
incident
(per
SD
increment;
hazard
ratio
1.78;
95%
CI
1.44,
2.20).
Compared
basic
(age
+
sex
race,
C-index,
0.627;
0.578,
0.675),
(C-index
increase
0.122;
0.071,
0.177),
CKD-PC
factors
0.175;
0.126,
0.217)
significantly
improved
prediction
CKD,
but
0.007;
−0.016,
0.025)
significant
improvement.
Adding
into
largest
C-index
0.825
0.802
to
0.825;
difference
0.023;
0.006,
0.044),
continuous
10-year
net
reclassification
(0.199;
0.059,
0.299)
integrated
discrimination
index
(0.041;
0.007,
0.083).
CONCLUSIONS
diabetes.
Язык: Английский
Multi-targeted olink proteomics analyses of cerebrospinal fluid from patients with aneurysmal subarachnoid hemorrhage
Proteome Science,
Год журнала:
2024,
Номер
22(1)
Опубликована: Ноя. 27, 2024
The
complexity
of
delayed
cerebral
ischemia
(DCI)
after
aneurysmal
subarachnoid
hemorrhage
(aSAH)
may
require
the
simultaneous
analysis
variant
types
protein
biomarkers
to
describe
it
more
accurately.
In
this
study,
we
analyzed
for
first
time
alterations
cerebrospinal
fluid
(CSF)
proteins
in
patients
with
aSAH
by
multi-targeted
Olink
proteomics,
aiming
reveal
pathophysiology
DCI
and
provide
insights
into
diagnosis
treatment
aSAH.
Six
six
control
were
selected,
CSF
samples
Proteomics
(including
96-neurology
panel
96-inflammation
panel)
based
on
Proximity
Extension
Assay
(PEA).
Differentially
expressed
(DEPs)
acquired
bioinformatics
was
performed.
PCA
revealed
better
intra-
inter-group
reproducibility
groups.
23
neurology-related
31
inflammation-relevant
differential
identified.
neurology
panel,
compared
controls,
up-regulated
SAH
predominantly
included
macrophage
scavenger
receptor
1
(MSR1),
siglec-1,
siglec-9,
cathepsin
C
(CTSC),
S
(CTSS),
etc.
Meanwhile,
inflammation
group,
incremental
mainly
contained
interleukin-6
(IL-6),
MCP-1,
CXCL10,
CXCL-9,
TRAIL,
Cluster
exhibited
significant
differences
between
two
GO
function
enrichment
hinted
that
pertinent
involved
regulation
defense
response,
vesicle-mediated
transport
immune
response;
while
related
largely
connected
cellular
response
chemokine,
chemokine
chemokine-mediated
signaling
pathway.
Additionally,
KEGG
indicated
significantly
enriched
phagosome,
apoptosis
microRNAs
cancer
And
pathway,
viral
interaction
cytokine
toll-like
These
identified
unique
pathophysiological
characteristics
secondary
Further
characterization
these
aberrant
pathways
future
research
could
enable
their
application
as
potential
therapeutic
targets
Язык: Английский
VASP, HCLS1, MSN, and EZR: Key molecular beacons in the pathophysiology of perihematomal edema Post-Intracerebral hemorrhage
Brain Hemorrhages,
Год журнала:
2024,
Номер
5(5), С. 223 - 232
Опубликована: Апрель 17, 2024
Perihematomal
edema
(PHE)
is
one
of
the
significant
secondary
cerebral
damages,
with
blood–brain
barrier's
integrity
playing
a
pivotal
role
in
its
progression.
Strengthening
tight
junction
(TJ)
proteins
enhances
barrier
integrity,
yet
complex
genetics
behind
brain
remain
not
fully
understood.
Our
research
endeavors
to
uncover
genes
and
their
roles
following
hemorrhage,
investigate
potential
treatment
strategies.
By
analyzing
intracerebral
hemorrhage
(ICH)
control
samples
using
GSE216607
GSE206971
datasets,
we
identified
differentially
expressed
genes.
Cross-referencing
KEGG
database,
aligned
these
those
related
junctions.
Extensive
enrichment
analysis
protein
interactions
were
performed
examine
expression
clinical
significance
study
employed
C57BL/6J
mouse
ICH
model
qRT-PCR
for
key
gene
validation.
Notably,
VASP,
HCLS1,
MSN,
EZR,
critical
junctions,
showed
increased
post-ICH,
emphasizing
BBB
upkeep
PHE
Drug
validation
indicated
therapeutic
effects
Testosterone
enanthate,
SELENIUM,
LY
294002
on
junction-related
This
sheds
light
involvement
progression
offering
promising
targets.
Further
needed
deeper
understanding.
Язык: Английский
Multiomics Profiling of Plasma Reveals Molecular Alterations Prior to a Diagnosis with Stroke Among Chinese Hypertension Patients
Journal of Proteome Research,
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 28, 2024
We
aimed
to
investigate
the
correlation
between
plasma
proteins
and
metabolites
occurrence
of
future
strokes
using
mass
spectrometry
bioinformatics
as
well
identify
other
biomarkers
that
could
predict
stroke
risk
in
hypertensive
patients.
In
a
nested
case-control
study,
baseline
samples
were
collected
from
50
subjects
who
developed
gender-,
age-
body
index-matched
controls.
Plasma
untargeted
metabolomics
data
independent
acquisition-based
proteomics
analysis
performed
patients,
19
111
found
be
differentially
expressed.
Integrative
analyses
revealed
molecular
changes
indicated
dysregulation
protein
digestion
absorption,
salivary
secretion,
regulation
actin
cytoskeleton,
along
with
significant
metabolic
suppression.
C4BPA,
Caprolactam,
Col15A1,
HBB
identified
predictors
occurrence,
Support
Vector
Machines
(SVM)
model
was
determined
optimal
predictive
by
integrating
six
machine-learning
classification
models.
The
SVM
showed
strong
performance
both
internal
validation
set
(area
under
curve
[AUC]:
0.977,
95%
confidence
interval
[CI]:
0.941-1.000)
external
(AUC:
0.973,
CI:
0.921-0.999).
Язык: Английский
Identification of Blood Biomarkers in Ischemic Stroke by Integrated Analysis of Metabolomics and Proteomics
Journal of Proteome Research,
Год журнала:
2024,
Номер
23(9), С. 4082 - 4094
Опубликована: Авг. 21, 2024
We
aimed
to
uncover
the
pathological
mechanism
of
ischemic
stroke
(IS)
using
a
combined
analysis
untargeted
metabolomics
and
proteomics.
The
serum
samples
from
discovery
set
44
IS
patients
matched
controls
were
analyzed
specific
detection
method.
same
method
was
then
used
validate
metabolites
proteins
in
two
validation
sets:
one
with
30
controls,
other
50
controls.
A
total
105
221
differentially
expressed
or
identified,
association
between
omics
determined
set.
Enrichment
top
25
two-way
orthogonal
partial
least-squares
discriminant
analysis,
which
employed
identify
highly
correlated
biomarkers,
highlighted
15
pathways
relevant
process.
One
metabolite
seven
exhibited
differences
groups
binary
logistic
regression
model,
included
2-hydroxyhippuric
acid
APOM_O95445,
MASP2_O00187,
PRTN3_D6CHE9,
achieved
an
area
under
curve
0.985
(95%
CI:
0.966–1)
This
study
elucidated
alterations
potential
coregulatory
influences
blood
patients.
Язык: Английский