Background:
Pancreatic
ductal
adenocarcinoma
(PDAC)
is
a
devastating
disease
with
limited
number
of
known
driver
mutations
but
considerable
cancer
cell
heterogeneity.
Phosphoproteomics
provides
direct
read-out
aberrant
signalling
and
the
resultant
clinically
relevant
phenotype.
Methods:
Mass
spectrometry
(MS)-based
proteomics
phosphoproteomics
were
applied
to
42
PDAC
tumors.
To
this
end,
protein
lysates
subjected
tryptic
digestion
sequential
phosphopeptide
capture
using
pY
antibodies
IMAC
beads
followed
by
nanoLC-MS/MS
database
searching.
Functional
data
mining
was
performed
Integrative
iNferred
Kinase
Activity
(INKA)
scoring,
ssGSEA
PTM-SEA.
subtypes
investigated
consensus
clustering.
The
collected
correlated
genomic
patient
survival
outcomes.
Findings:
Data
encompassed
over
19936
pS/T
(in
5412
phosphoproteins)
1208
sites
501
total
3756
proteins.
Proteome
identified
three
distinct
tumor
intrinsic
stromal
features.
Subsequently,
phospho-subtypes
apparent:
two
tumour-intrinsic
(Phos1/2)
one
(Phos3),
resembling
molecular
subtypes.
Phos
displayed
differential
phosphorylation
signals
kinase
activity,
such
as
FGR
GSK3
activation
in
Phos1,
SRC
family
EPHA2
Phos2,
EGFR,
INSR,
MET,
ABL1,
HIPK1,
JAK
PRKCD
Phos3.
activity
analysis
an
external
cohort
supported
our
findings
underscored
importance
PI3K/AKT
ERK
pathways,
among
other.
Interestingly,
unfavorable
prognosis
higher
RTK,
MAPK
CDK
high
proliferation,
whereas
long
associated
MYLK,
ILK,
PTK6
previously
unknown.
Interpretation:
Subtype-associated
profiles
can
guide
therapeutic
combination
approaches
tumour
stroma
enriched
tissues,
emphasize
critical
role
parallel
pathways.
In
addition,
profiling
identifies
potential
markers
prognostic
significance.Funding:
This
project
Dutch
Cancer
Society
(KWF
Kankerbestrijding,
grant
KWF2016-1
/
10212
C.R.J.,
M.F.B.
E.G.).
Center
Amsterdam
Netherlands
Organisation
for
Scientific
Research
(NWO-Middelgroot
91116017)
are
acknowledged
support
mass
infrastructure
Surfsara
computing
(reference
e-infra180166).Declaration
Interest:
has
received
research
funding
from
Celgene,
Frame
Therapeutics,
Lead
Pharma.
He
acted
consultant
Servier.
Ethical
Approval:
Tumor
tissue
specimens,
snap-frozen
liquid
nitrogen
stored
at
-80°C,
retrospectively
archive
Department
Pathology
(approved
Committee
Review
Biobanks,
CTB.2015-081)
purpose
phosphoproteomic
research.
Retrospective
collection
conducted
accordance
ethical
guidelines
UMC
Code,
based
on
'Code
conduct
Health
Research'
(Dutch
Regulation
Research).
International Journal of Molecular Sciences,
Journal Year:
2023,
Volume and Issue:
24(16), P. 12613 - 12613
Published: Aug. 9, 2023
Our
understanding
of
the
molecular
mechanisms
underlying
cancer
development
and
evolution
have
evolved
rapidly
over
recent
years,
variation
from
one
patient
to
another
is
now
widely
recognized.
Consequently,
one-size-fits-all
approaches
treatment
been
superseded
by
precision
medicines
that
target
specific
disease
characteristics,
promising
maximum
clinical
efficacy,
minimal
safety
concerns,
reduced
economic
burden.
While
oncology
has
very
successful
in
some
tumors
with
a
large
number
patients
do
not
yet
access
for
their
disease.
The
success
next-generation
depends
on
discovery
new
actionable
rapid,
accurate,
comprehensive
diagnosis
complex
phenotypes
within
each
patient,
novel
trial
designs
improved
response
rates,
worldwide
targeted
anticancer
therapies
all
patients.
This
review
outlines
current
technological
trends,
highlights
multidisciplinary
efforts
are
underway
ensure
many
more
will
be
able
benefit
near
future.
International Journal of Molecular Sciences,
Journal Year:
2024,
Volume and Issue:
25(16), P. 8621 - 8621
Published: Aug. 7, 2024
Inflammation
is
activated
by
diverse
triggers
that
induce
the
expression
of
cytokines
and
adhesion
molecules,
which
permit
a
succession
molecules
cells
to
deliver
stimuli
functions
help
immune
system
clear
primary
cause
tissue
damage,
whether
this
an
infection,
tumor,
or
trauma.
During
inflammation,
short-term
changes
in
secretion
strong
mediators
inflammation
occur,
while
long-term
occur
specific
groups
cells.
Long-term
include
cellular
transdifferentiation
for
some
types
need
regenerate
damaged
tissue,
as
well
death
can
be
detrimental
integrity
if
they
remain
active
beyond
boundaries
essential
function.
The
transcriptional
regulator
NFκB
enables
fundamental
gene
during
development.
recurrence
malignant
disease,
cell
stress-induced
alterations
enable
growth
cancer
clones
are
substantially
resistant
therapeutic
intervention
system.
A
number
those
due
significant
defects
feedback
signal
cascades
control
activity
NFκB.
Specifically,
stress
contributes
it
overrides
modules
otherwise
protect
host
tissue.
involved
both
suppression
promotion
cancer,
key
distinctive
feature
determines
its
net
effect
remains
unclear.
This
paper
aims
provide
answer
at
least
one
aspect
question,
namely
mechanism
divergent
response
critical
inflammatory
general.
International Journal of Molecular Sciences,
Journal Year:
2025,
Volume and Issue:
26(2), P. 722 - 722
Published: Jan. 16, 2025
The
COVID-19
pandemic
has
accelerated
advances
in
molecular
biology
and
virology,
enabling
the
identification
of
key
biomarkers
to
differentiate
between
severe
mild
cases.
Furthermore,
use
artificial
intelligence
(AI)
machine
learning
(ML)
analyze
large
datasets
been
crucial
for
rapidly
identifying
relevant
disease
prognosis,
including
COVID-19.
This
approach
enhances
diagnostics
emergency
settings,
allowing
more
accurate
efficient
patient
management.
study
demonstrates
how
algorithms
departments
can
identify
vital
prognosis
an
emerging
using
as
example
by
analyzing
clinical,
epidemiological,
analytical,
radiological
data.
All
consecutively
admitted
patients
were
included,
than
89
variables
processed
Random
Forest
(RF)
algorithm.
RF
model
achieved
highest
balanced
accuracy
at
92.61%.
most
predictive
mortality
included
procalcitonin
(PCT),
lactate
dehydrogenase
(LDH),
C-reactive
protein
(CRP).
Additionally,
system
highlighted
significance
interstitial
infiltrates
chest
X-rays
D-dimer
levels.
Our
results
demonstrate
that
is
critical
diseases,
accelerating
data
analysis,
optimizing
personalized
treatment,
emphasizing
importance
PCT
LDH
high-risk
patients.
Cell Communication and Signaling,
Journal Year:
2025,
Volume and Issue:
23(1)
Published: March 13, 2025
Abstract
Background
The
P21
activated
kinases
(PAK)
are
frequently
dysregulated
in
cancer
and
have
central
roles
oncogenic
signalling,
prompting
the
development
of
PAK
inhibitors
(PAKi)
as
anticancer
agents.
However,
such
compounds
not
reached
clinical
use
because,
at
least
partially,
there
is
a
limited
mechanistic
understanding
their
mode
action.
Here,
we
aimed
to
characterize
functional
molecular
responses
PAKi
(PF-3758309,
FRAX-486
IPA-3)
multiple
acute
myeloid
leukaemia
(AML)
models
gain
insights
on
biochemical
pathways
affected
by
these
this
disease
identify
determinants
response
patient
samples.
Methods
We
mined
phosphoproteomic
datasets
primary
AML,
used
proteomics
phosphoproteomics
profile
impact
immortalized
(P31/Fuj
MV4-11),
AML
cells
from
8
patients.
These
omics
were
integrated
with
gene
dependency
data
which
proteins
targeted
necessary
for
proliferation
AML.
studied
effect
cell
cycle
progression,
proliferation,
differentiation
apoptosis.
Finally,
input
machine
learning
that
predicted
ex
vivo
two
independent
(with
36
50
cases,
respectively)
PF-3758309
markers
response.
Results
found
PAK1
activation–
measured
data–
was
predictive
poor
prognosis
cases.
most
effective
reducing
inducing
apoptosis
lines.
In
lines
cells,
inhibited
PAK,
AMPK
PKCA
activities,
reduced
c-MYC
transcriptional
activity
expression
ribosomal
proteins,
FLT3
pathway
FLT3-ITD
mutated
cells.
STAT5
phosphorylation
Tyr699.
Functionally,
cell-growth,
induced
apoptosis,
blocked
progression
promoted
model-dependent
manner.
ML
modelling
accurately
classified
samples
sensitive
or
resistant
treatment,
highlighted
PHF2
Ser705
robust
biomarker.
Conclusions
summary,
our
define
proteomic,
immortalised
suggest
route
personalise
treatments
based
inhibitors.
Hematology Reports,
Journal Year:
2025,
Volume and Issue:
17(2), P. 18 - 18
Published: March 28, 2025
Leukemia
is
a
heterogeneous
group
of
hematologic
malignancies
characterized
by
distinct
genetic
and
molecular
abnormalities.
Advancements
in
genomic
technologies
have
significantly
transformed
the
diagnosis,
prognosis,
treatment
strategies
for
leukemia.
Among
these,
next-generation
sequencing
(NGS)
has
emerged
as
powerful
tool,
enabling
high-resolution
profiling
that
surpasses
conventional
diagnostic
approaches.
By
providing
comprehensive
insights
into
mutations,
clonal
evolution,
resistance
mechanisms,
NGS
revolutionized
precision
medicine
leukemia
management.
Despite
its
transformative
potential,
clinical
integration
presents
challenges,
including
data
interpretation
complexities,
standardization
issues,
cost
considerations.
However,
continuous
advancements
platforms
bioinformatics
pipelines
are
enhancing
reliability
accessibility
routine
practice.
The
expanding
role
paving
way
improved
risk
stratification,
targeted
therapies,
real-time
disease
monitoring,
ultimately
leading
to
better
patient
outcomes.
This
review
highlights
impact
on
research
applications,
discussing
advantages
over
traditional
techniques,
key
approaches,
emerging
challenges.
As
oncology
continues
evolve,
expected
play
an
increasingly
central
diagnosis
management
leukemia,
driving
innovations
personalized
therapeutic
interventions.
Cancers,
Journal Year:
2023,
Volume and Issue:
16(1), P. 8 - 8
Published: Dec. 19, 2023
AML
is
a
highly
aggressive
and
heterogeneous
form
of
hematological
cancer.
Proteomics-based
stratification
patients
into
more
refined
subgroups
may
contribute
to
precise
characterization
the
patient-derived
cells.
Here,
we
reanalyzed
liquid
chromatography-tandem
mass
spectrometry
(LC-MS/MS)
generated
proteomic
phosphoproteomic
data
from
26
FAB-M4/M5
patients.
The
achieved
complete
remission
after
induction
therapy.
Twelve
them
later
developed
chemoresistant
relapse
(RELAPSE),
14
were
relapse-free
(REL_FREE)
long-term
survivors.
We
considered
not
only
RELAPSE
REL_FREE
characteristics
but
also
integrated
French-American-British
(FAB)
classification,
along
with
considering
presence
nucleophosmin
1
(NPM1)
mutation
cytogenetically
normal
AML.
found
significant
number
differentially
enriched
proteins
(911)
phosphoproteins
(257)
between
various
FAB
subtypes
in
Patients
myeloblastic
M1/M2
subtype
showed
higher
levels
RNA
processing-related
routes
lower
signaling
related
terms
like
translation
degranulation
when
compared
M4/M5
subtype.
Moreover,
that
high
abundance
associated
mitochondrial
oxidative
phosphorylation,
particularly
observed
NPM1
mutated
subgroup,
distinguishes
relapsing
non-relapsing
patient
cells
M4/M5.
Thus,
discovery
subtype-specific
biomarkers
through
profiling
complement
existing
classification
system
for
potentially
aid
selecting
personalized
treatment
strategies
individual
Frontiers in Pharmacology,
Journal Year:
2024,
Volume and Issue:
15
Published: Aug. 5, 2024
Acute
myeloid
leukemia
(AML),
an
aggressive
malignancy
of
hematopoietic
stem
cells,
is
characterized
by
the
blockade
cell
differentiation,
uncontrolled
proliferation,
and
expansion
that
impairs
healthy
hematopoiesis
results
in
pancytopenia
susceptibility
to
infections.
Several
genetic
chromosomal
aberrations
play
a
role
AML
influence
patient
outcomes.
TP53
key
tumor
suppressor
gene
involved
variety
features,
such
as
cell-cycle
regulation,
genome
stability,
stem-cell
homeostasis,
apoptosis,
metabolism,
senescence,
repair
DNA
damage
response
cellular
stress.
In
AML,
alterations
occur
5%-12%
de
novo
cases.
These
mutations
form
important
molecular
subgroup,
patients
with
these
have
worst
prognosis
shortest
overall
survival
among
even
when
treated
chemotherapy
allogeneic
transplant.
The
frequency
TP53-mutations
increases
relapsed
recurrent
associated
chemoresistance.
Progress
genetics
biology
has
brought
novel
therapies,
however,
clinical
benefit
agents
for
whose
disease
driven
remains
largely
unexplored.
This
review
focuses
on
characteristics
TP53-mutated
disease;
impact
selected
hallmarks
leukemia,
particularly
metabolic
rewiring
immune
evasion,
importance
mutations;
current
progress
development
preclinical
therapeutic
strategies
treat
disease.