Communications Biology,
Год журнала:
2023,
Номер
6(1)
Опубликована: Окт. 19, 2023
Abstract
In
today’s
post-genomic
era,
it
is
crucial
to
rethink
the
concept
of
model
organisms.
While
a
few
historically
well-established
organisms,
e.g.
laboratory
rodents,
have
enabled
significant
scientific
breakthroughs,
there
now
pressing
need
for
broader
inclusion.
Indeed,
new
organisms
and
models,
from
complex
microbial
communities
holobionts,
are
essential
fully
grasp
complexity
biological
principles
across
breadth
biodiversity.
By
fostering
collaboration
between
biology,
advanced
molecular
science
omics
communities,
we
can
collectively
adopt
unraveling
their
functioning,
uncovering
fundamental
mechanisms.
This
concerted
effort
will
undoubtedly
enhance
human
health,
environmental
quality,
biodiversity
conservation.
Biomedicines,
Год журнала:
2025,
Номер
13(1), С. 152 - 152
Опубликована: Янв. 9, 2025
Background/Objectives:
Hepatocellular
carcinoma
(HCC)
remains
a
significant
global
health
concern,
primarily
due
to
the
limited
efficacy
of
targeted
therapies,
which
are
often
compromised
by
drug
resistance
and
adverse
side
effects.
Methods:
In
this
study,
we
utilized
Tandem
Mass
Tag
(TMT)-based
quantitative
proteomic
approach
analyze
protein
expression
serine/threonine/tyrosine
(S/T/Y)
phosphorylation
modifications
in
HepG2
cells
following
treatment
with
three
clinically
relevant
hepatocellular
carcinoma-targeted
agents:
apatinib,
regorafenib,
lenvatinib.
Results:
Utilizing
KEGG
pathway
enrichment
analysis,
biological
process
interaction
network
elucidated
common
specific
metabolic
pathways,
processes,
regulatory
networks
influenced
liver
cancer
therapeutics.
The
study
additionally
proposed
potential
combinational
strategies,
highlighting
possible
synergistic
between
HCC-targeted
drugs
DNA
methyltransferase
inhibitor.
Furthermore,
through
integration
clinical
site
data,
identified
several
sites
that
exhibited
higher
abundance
tumor
tissues
compared
adjacent
non-tumor
tissues.
These
were
associated
poor
prognosis
elevated
functional
scores.
Conclusions:
summary,
conducted
an
in-depth
analysis
molecular
alterations
proteins
induced
drugs,
predicting
combination
strategies
therapeutic
targets.
Medicinal Research Reviews,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 9, 2025
ABSTRACT
Proteins
hold
pivotal
importance
since
many
diseases
manifest
changes
in
protein
activity.
Proteomics
techniques
provide
a
comprehensive
exploration
of
structure,
abundance,
and
function
biological
samples,
enabling
the
holistic
characterization
overall
organisms.
Nowadays,
breadth
emerging
methodologies
proteomics
is
unprecedentedly
vast,
with
constant
optimization
technologies
sample
processing,
data
collection,
analysis,
its
scope
application
steadily
transitioning
from
bench
to
clinic.
Here,
we
offer
an
insightful
review
technical
developments
applications
biomedicine
over
past
5
years.
We
focus
on
profound
contributions
profiling
disease
spectra,
discovering
new
biomarkers,
identifying
promising
drug
targets,
deciphering
alterations
conformation,
unearthing
protein–protein
interactions.
Moreover,
summarize
cutting‐edge
potential
breakthroughs
pipeline
principal
challenges
proteomics.
Based
these,
aspire
broaden
applicability
inspire
researchers
enhance
our
understanding
complex
systems
by
utilizing
such
techniques.
Clinical and Translational Medicine,
Год журнала:
2025,
Номер
15(3)
Опубликована: Март 1, 2025
Oral
squamous
cell
carcinoma
(OSCC)
is
an
increasingly
prevalent
malignancy
worldwide.
This
study
aims
to
understand
molecular
alterations
associated
with
lymph
node
metastasis
of
OSCC
in
order
improve
treatment
strategies.
We
analysed
a
cohort
46
patients
primary
OSCC,
including
10
and
36
without.
Using
comprehensive
multi-omics
approach
-
encompassing
genomic,
transcriptomic,
proteomic,
epigenetic,
single-cell,
spatial
analyses
we
integrated
data
delineate
the
landscape
context
metastasis.
Our
genomic
analysis
identified
significant
mutations
key
genes
within
MAPK,
TGF-β
WNT
signalling
pathways,
which
are
essential
for
tumour
development.
The
proteogenomic
highlighted
pathways
critical
dissemination
factors
contributing
immunosuppressive
microenvironment.
Elevated
levels
POSTN
were
found
reorganise
extracellular
matrix
(ECM),
interact
TGF-β,
disrupt
cycle
regulation
suppress
immune
response
by
reducing
VCAM1
activity.
Integrated
single-cell
transcriptome
revealed
that
cancer-associated
fibroblasts
(CAFs)
secrete
TGF-β1/2,
promoting
cancer
through
epithelial-mesenchymal
transition
(EMT).
provides
detailed
understanding
mechanisms
driving
OSCC.
These
insights
could
lead
more
precise
diagnostics
targeted
treatments.
article
protected
copyright.
All
rights
reserved.
Analytical Chemistry,
Год журнала:
2023,
Номер
95(3), С. 1888 - 1898
Опубликована: Янв. 13, 2023
There
is
a
growing
demand
to
develop
high-throughput
and
high-sensitivity
mass
spectrometry
methods
for
single-cell
proteomics.
The
commonly
used
isobaric
labeling-based
multiplexed
proteomics
approach
suffers
from
distorted
protein
quantification
due
co-isolated
interfering
ions
during
MS/MS
fragmentation,
also
known
as
ratio
compression.
We
reasoned
that
the
use
of
MS3-based
could
mitigate
compression
provide
better
quantification.
However,
previous
studies
indicated
reduced
proteome
coverages
in
MS3
method,
likely
long
duty
cycle
time
ion
losses
multilevel
selection
fragmentation.
Herein,
we
described
an
improved
MS
acquisition
method
by
employing
linear
trap
measure
reporter
ions.
demonstrated
can
increase
single-cell-level
peptides
with
even
higher
gain
obtained
via
method.
optimized
real-time
search
was
further
applied
study
immune
activation
single
macrophages.
Among
total
126
cells
studied,
over
1200
1000
proteins
were
quantifiable
when
at
least
50
75%
nonmissing
data
required,
respectively.
Our
evaluation
revealed
several
limitations
low-resolution
detector
suggested
experimental
solutions
minimize
their
impacts
on
analysis.
Communications Biology,
Год журнала:
2023,
Номер
6(1)
Опубликована: Окт. 19, 2023
Abstract
In
today’s
post-genomic
era,
it
is
crucial
to
rethink
the
concept
of
model
organisms.
While
a
few
historically
well-established
organisms,
e.g.
laboratory
rodents,
have
enabled
significant
scientific
breakthroughs,
there
now
pressing
need
for
broader
inclusion.
Indeed,
new
organisms
and
models,
from
complex
microbial
communities
holobionts,
are
essential
fully
grasp
complexity
biological
principles
across
breadth
biodiversity.
By
fostering
collaboration
between
biology,
advanced
molecular
science
omics
communities,
we
can
collectively
adopt
unraveling
their
functioning,
uncovering
fundamental
mechanisms.
This
concerted
effort
will
undoubtedly
enhance
human
health,
environmental
quality,
biodiversity
conservation.
