medRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 2, 2024
ABSTRACT
Background
Hepatocellular
carcinoma
(HCC)
is
one
of
the
most
common
and
lethal
malignancies
worldwide.
HCC
diagnosis,
monitoring,
treatment
decisions
rely
predominantly
on
imaging.
Curative
surgery
limited
to
those
with
disease
confined
liver,
but
recurrence
common.
Detection
by
mutational
profiling
blood
plasma
cell-free
DNA
(cfDNA)
heterogeneity
difficulty
obtaining
tumor
tissue
guide
targeted
gene
panels.
In
contrast,
methylation
patterns
reveal
biological
processes
without
need
for
prior
knowledge.
We
evaluated
methylated
immunoprecipitation
high-throughput
sequencing
(cfMeDIP-Seq)
detection
monitoring
after
curative-intent
surgery.
Methods
identified
patients
undergoing
liver
transplantation
or
resection
collected
at
(baseline)
every
3
months
two
years
(follow-up).
performed
cfMeDIP-Seq
followed
machine
learning
i)
develop
an
classifier
based
300
differentially
regions
in
a
Discovery
cohort
35
living
donors
(healthy
controls)
52
baseline
samples
from
patients;
ii)
test
separate
Validation
37
112
follow-up
iii)
assign
score
(HMS)
their
probability
(0.0-1.0)
containing
HCC-derived
cfDNA.
assessed
relationships
between
HMS
clinical
variables.
Results
depth
101-129
(median
113)
million
reads
per
sample
succeeded
201
89
(57
transplant
32
resection)
healthy
controls.
cohort,
97%
sensitivity
99%
specificity
(mean
AUROC
=
0.999).
accuracy
distinguished
samples,
follow-ups
recurrence,
Baseline
HMS>0.9
was
associated
higher
risk
Cox
regression
(HR
3.43
(95%
CI
1.30-9.06),
p=0.013).
all
decreased
3-44%
17%)
within
first
13
weeks
Subsequently,
trajectory
recurrent
non-recurrent
diverged,
rise
relative
post-surgery
timepoint
recurrence.
functioned
independently
other
clinicopathologic
Conclusion
Tumor-agnostic
cfDNA
methylomes
accurately
detect
predict
transplantation.
This
approach
may
have
important
implications
treatment,
monitoring.
Signal Transduction and Targeted Therapy,
Год журнала:
2025,
Номер
10(1)
Опубликована: Фев. 6, 2025
Abstract
Liver
cancer
represents
a
major
global
health
concern,
with
projections
indicating
that
the
number
of
new
cases
could
surpass
1
million
annually
by
2025.
Hepatocellular
carcinoma
(HCC)
constitutes
around
90%
liver
and
is
primarily
linked
to
factors
incluidng
aflatoxin,
hepatitis
B
(HBV)
C
(HCV),
metabolic
disorders.
There
are
no
obvious
symptoms
in
early
stage
HCC,
which
often
leads
delays
diagnosis.
Therefore,
HCC
patients
usually
present
tumors
advanced
incurable
stages.
Several
signaling
pathways
dis-regulated
cause
uncontrolled
cell
propagation,
metastasis,
recurrence
HCC.
Beyond
frequently
altered
therapeutically
targeted
receptor
tyrosine
kinase
(RTK)
involved
differentiation,
telomere
regulation,
epigenetic
modification
stress
response
also
provide
therapeutic
potential.
Investigating
key
their
inhibitors
pivotal
for
achieving
advancements
management
At
present,
primary
approaches
(TKI),
immune
checkpoint
(ICI),
combination
regimens.
New
trials
investigating
therapies
involving
ICIs
TKIs
or
anti-VEGF
(endothelial
growth
factor)
therapies,
as
well
combinations
two
immunotherapy
The
outcomes
these
expected
revolutionize
across
all
Here,
we
here
comprehensive
review
cellular
pathways,
potential,
evidence
derived
from
late-stage
clinical
discuss
concepts
underlying
earlier
trials,
biomarker
identification,
development
more
effective
therapeutics
Cell Research,
Год журнала:
2025,
Номер
35(1), С. 11 - 22
Опубликована: Янв. 3, 2025
Abstract
Genomic
instability
is
a
hallmark
of
cancer
and
major
driving
force
tumorigenesis.
A
key
manifestation
genomic
the
formation
extrachromosomal
DNAs
(ecDNAs)
—
acentric,
circular
DNA
molecules
ranging
from
50
kb
to
5
Mb
in
size,
distinct
chromosomes.
Ontological
studies
have
revealed
that
ecDNA
serves
as
carrier
oncogenes,
immunoregulatory
genes,
enhancers,
capable
elevated
transcription
its
cargo
genes
heterogeneity,
leading
rapid
tumor
evolution
therapy
resistance.
Although
was
documented
over
half
century
ago,
past
decade
has
witnessed
surge
breakthrough
discoveries
about
biological
functions.
Here,
we
systematically
review
modern
biology
uncovered
last
ten
years,
focusing
on
how
during
this
pioneering
stage
illuminated
our
understanding
ecDNA-driven
transcription,
progression.
Furthermore,
discuss
ongoing
efforts
target
novel
approach
therapy.
This
burgeoning
field
entering
new
phase,
poised
reshape
knowledge
therapeutic
strategies.
Cancers,
Год журнала:
2024,
Номер
16(8), С. 1582 - 1582
Опубликована: Апрель 20, 2024
Hepatocellular
carcinoma
(HCC)
is
the
most
common
form
of
liver
cancer,
accounting
for
~90%
neoplasms.
It
second
leading
cause
cancer-related
deaths
and
seventh
cancer
worldwide.
Although
there
have
been
rapid
developments
in
treatment
HCC
over
past
decade,
incidence
mortality
rates
remain
a
challenge.
With
widespread
use
hepatitis
B
vaccine
antiviral
therapy,
etiology
shifting
more
toward
metabolic-associated
steatohepatitis
(MASH).
Early-stage
can
be
treated
with
potentially
curative
strategies
such
as
surgical
resection,
transplantation,
radiofrequency
ablation,
improving
long-term
survival.
However,
patients,
when
diagnosed,
are
already
intermediate
or
advanced
stages.
Molecular
targeted
followed
by
immune
checkpoint
inhibitor
immunotherapy,
has
revolution
systemic
treatment.
Systemic
especially
patients
compromised
function
still
challenge
due
to
significant
resistance
blockade,
tumor
heterogeneity,
lack
oncogenic
addiction,
effective
predictive
therapeutic
biomarkers.
Pathogens,
Год журнала:
2024,
Номер
13(5), С. 362 - 362
Опубликована: Апрель 27, 2024
The
hepatitis
D
virus
(HDV)
is
a
compact,
enveloped,
circular
RNA
that
relies
on
B
(HBV)
envelope
proteins
to
initiate
primary
infection
in
hepatocytes,
assemble,
and
secrete
new
virions.
Globally,
HDV
affects
an
estimated
12
million
72
people,
carrying
significantly
elevated
risk
of
developing
cirrhosis,
liver
failure,
hepatocellular
carcinoma
(HCC)
compared
HBV
mono-infection.
Furthermore,
HDV-associated
HCC
often
manifests
at
younger
age
exhibits
more
aggressive
characteristics.
intricate
mechanisms
driving
the
synergistic
carcinogenicity
are
not
fully
elucidated
but
believed
involve
chronic
inflammation,
immune
dysregulation,
direct
oncogenic
effects
HDV.
Indeed,
recent
data
highlight
molecular
profile
associated
with
unique
distinct
from
HBV-induced
HCC.
However,
question
whether
remains
unanswered.
In
this
review,
we
comprehensively
examined
several
crucial
aspects
HDV,
encompassing
its
epidemiology,
biology,
immunology,
risks
disease
progression
development.
Frontiers in Oncology,
Год журнала:
2024,
Номер
14
Опубликована: Май 8, 2024
Elevated
plasma
fibrinogen
(Fg)
levels
consistently
correlate
with
an
unfavorable
prognosis
in
various
tumor
patient
cohorts.
Within
the
microenvironment,
aberrant
deposition
and
expression
of
Fg
have
been
observed,
interacting
multiple
cellular
receptors
thereby
accentuating
its
role
as
a
regulator
inflammatory
processes.
Specifically,
serves
to
stimulate
recruit
immune
cells
pro-inflammatory
cytokines,
contributing
promotion
progression.
Additionally,
fragments
exhibit
dichotomous
effects
on
angiogenesis.
Notably,
also
facilitates
migration
through
both
platelet-dependent
platelet-independent
mechanisms.
Recent
studies
illuminated
several
tumor-related
signaling
pathways
influenced
by
Fg.
This
review
provides
comprehensive
summary
intricate
involvement
biology,
elucidating
multifaceted
underlying
BioMedInformatics,
Год журнала:
2024,
Номер
4(3), С. 1757 - 1772
Опубликована: Июль 24, 2024
In
this
scoping
review,
we
delve
into
the
transformative
potential
of
artificial
intelligence
(AI)
in
addressing
challenges
inherent
whole-genome
sequencing
(WGS)
analysis,
with
a
specific
focus
on
its
implications
oncology.
Unveiling
limitations
existing
technologies,
review
illuminates
how
AI-powered
methods
emerge
as
innovative
solutions
to
surmount
these
obstacles.
The
evolution
DNA
progressing
from
Sanger
next-generation
sequencing,
sets
backdrop
for
AI’s
emergence
potent
ally
processing
and
analyzing
voluminous
genomic
data
generated.
Particularly,
deep
learning
play
pivotal
role
extracting
knowledge
discerning
patterns
vast
landscape
information.
context
oncology,
exhibit
considerable
across
diverse
facets
WGS
including
variant
calling,
structural
variation
identification,
pharmacogenomic
analysis.
This
underscores
significance
multimodal
approaches
diagnoses
therapies,
highlighting
importance
ongoing
research
development
techniques.
Integrating
AI
analytical
framework
empowers
scientists
clinicians
unravel
intricate
interplay
genomics
within
realm
multi-omics
research,
paving
way
more
successful
personalized
targeted
treatments.
Nucleic Acids Research,
Год журнала:
2025,
Номер
53(1)
Опубликована: Янв. 7, 2025
Abstract
Most
of
the
risk
factors
associated
with
chronic
and
complex
diseases,
such
as
cancer,
stem
from
exogenous
endogenous
exposures
experienced
throughout
an
individual’s
life,
collectively
known
exposome.
These
can
modify
DNA,
which
subsequently
lead
to
somatic
mutations
found
in
all
normal
tumor
tissues.
Understanding
precise
origins
specific
has
been
challenging
due
multitude
DNA
adducts
(i.e.
adductome)
their
diverse
positions
within
genome.
Thus
far,
this
limitation
prevented
researchers
precisely
linking
subsequent
mutational
outcomes.
Indeed,
many
common
observed
human
cancers
appear
originate
error-prone
processes.
Consequently,
it
remains
unclear
whether
these
result
exposure-induced
adducts,
or
arise
indirectly
processes
are
a
combination
both.
In
review,
we
summarize
approaches
that
aim
bridge
our
understanding
mechanism
by
exposure
leads
damage
then
mutation
highlight
some
remaining
challenges
shortcomings
fully
supporting
paradigm.
We
emphasize
need
integrate
cellular
adductomics,
long
read-based
mapping,
single-molecule
duplex
sequencing
native
molecules
advanced
computational
analysis.
This
proposed
holistic
approach
aims
unveil
causal
connections
between
key
modifications
landscape,
they
external
exposures,
internal
both,
thereby
addressing
questions
cancer
biology.
Molecular Biology and Evolution,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 17, 2025
Abstract
The
study
of
mutational
processes
in
somatic
genomes
has
gained
recent
momentum,
uncovering
a
wide
array
endogenous
and
exogenous
factors
associated
with
changes.
However,
the
overall
landscape
germline
mutations
across
tree
life
evolutionary
driving
forces
are
rather
unclear.
In
this
study,
we
analyzed
single-stranded
RNA
(ssRNA)
viruses
which
known
to
jump
between
different
hosts
divergent
environments.
We
found
that
spectra
ssRNA
differ
significantly
mainly
their
genetic
divergence.
Surprisingly,
host
environments
contribute
much
less
spectrum,
challenging
prevailing
view
cellular
environment
is
major
determinant
spectrum
viruses.
To
dissect
shaping
viral
spectra,
selected
two
important
scenarios,
namely
inter-host
evolution
strains
as
well
intra-host
evolution.
both
change
through
space
time,
strongly
correlating
levels
natural
selection.
Combining
all
viruses,
identified
suite
signatures
varying
degrees
similarity
humans,
indicating
universal
life.
Taken
together,
unraveled
an
unprecedented
dynamic
pinpointing
fast
species.
Transplantation Direct,
Год журнала:
2025,
Номер
11(2), С. e1746 - e1746
Опубликована: Янв. 23, 2025
Background.
Hepatocellular
carcinoma
(HCC)
has
a
rising
incidence
and
mortality
in
North
America.
Liver
transplantation
(LT)
with
adjunctive
therapies
offers
excellent
outcomes.
However,
HCC
recurrences
are
associated
high
mortality.
We
investigate
whether
adjuvant
systemic
therapy
can
reduce
recurrence,
as
shown
other
malignancies.
Methods.
Medical
records
of
patients
undergoing
LT
for
at
single
center
between
January
2016
December
2022
were
retrospectively
reviewed.
Patients
stratified
into
3
groups:
(1)
recipients
sorafenib,
(2)
nonrecipients
recurrence
risk,
(3)
low
risk
by
explant
pathology
features.
The
outcomes
overall
survival
(OS)
recurrence-free
(RFS).
Adjuvant
sorafenib
also
propensity
score
matched
1:2
to
nonadjuvant
based
on
Results.
During
the
study
period,
273
underwent
16
(5.9%)
received
therapy.
demographically
similar
and,
pathology,
had
greater
tumor
burden,
lymphovascular
invasion,
poorer
differentiation
(all
P
<
0.001).
Adverse
events
observed
12
(75%).
OS
was
among
groups
(
=
0.2),
not
multivariable
analysis
(hazard
ratio,
1.31;
95%
confidence
interval,
0.45-3.78;
0.62).
RFS
significantly
lower
6.99;
2.12-23.05;
Following
matching,
use
either
0.24)
or
rates
0.65).
Conclusions.
In
this
single-center
analysis,
OS.
Recipients
have
shorter
RFS,
likely
due
increased
prevalence
high-risk
features,
frequencies
adverse
events.