bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 17, 2025
Abstract
High-dimensional
sequencing
data,
such
as
RNA-Seq
for
gene
expression
and
ATAC-Seq
chromatin
accessibility,
are
widely
used
in
studying
systems
biology.
Accessible
allows
transcription
factors
regulatory
elements
to
bind
DNA,
thereby
regulating
through
the
activation
or
repression
of
target
genes.
The
association
analysis
data
provides
insights
into
mechanisms.
Most
existing
analytic
tools
exclusively
focus
on
cis-associations,
despite
being
able
physically
interact
with
distant
Furthermore,
conventional
approaches
often
utilize
Pearson
Spearman
correlations,
which
ignore
count-based
nature
data.
To
address
these
limitations,
we
introduce
PETScan
,
a
computationally
efficient
genome-wide
PE
ak-
T
ranscript
Sc
ore-based
an
alysis,
utilizing
negative
binomial
models
better
accommodate
We
leverage
score
tests
matrix
calculations
improved
computational
efficiency,
combine
empirical
permutation
method
genomic
control
ensure
valid
p-value
studies
limited
sample
sizes.
In
real-world
datasets,
achieved
three
orders
magnitude
faster
than
Wald
tests,
while
identifying
similar
significant
gene-peak
pairs.
R
package
is
available
GitHub
at
https://github.com/yajing-hao/PETScan
.
Genes,
Journal Year:
2025,
Volume and Issue:
16(1), P. 93 - 93
Published: Jan. 17, 2025
Male
reproductive
health
is
governed
by
an
intricate
interplay
of
genetic,
epigenetic,
and
environmental
factors.
Epigenetic
mechanisms—encompassing
DNA
methylation,
histone
modifications,
non-coding
RNA
activity—are
crucial
both
for
spermatogenesis
sperm
maturation.
However,
oxidative
stress,
driven
excessive
reactive
oxygen
species,
disrupts
these
processes,
leading
to
impaired
function
male
infertility.
This
disruption
extends
epigenetic
resulting
in
abnormal
gene
expression
chromatin
remodeling
that
compromise
genomic
integrity
fertilization
potential.
Importantly,
oxidative-stress-induced
alterations
can
be
inherited,
affecting
the
fertility
offspring
future
generations.
review
investigates
how
stress
influences
regulation
reproduction
modifying
RNAs,
ultimately
compromising
spermatogenesis.
Additionally,
it
discusses
transgenerational
implications
disruptions
their
potential
role
hereditary
infertility
disease
predisposition.
Understanding
mechanisms
vital
developing
therapeutic
strategies
mitigate
damage
restore
homeostasis
germline.
By
integrating
insights
from
molecular,
clinical,
research,
this
work
emphasizes
need
targeted
interventions
enhance
prevent
adverse
outcomes
progeny.
Furthermore,
elucidating
dose–response
relationships
between
changes
remains
a
critical
research
priority,
informing
personalized
diagnostics
interventions.
In
context,
studies
should
adopt
standardized
markers
damage,
robust
clinical
trials,
multi-omic
approaches
capture
complexity
Such
rigorous
investigations
will
reduce
risk
disorders
optimize
outcomes.
International Journal of Biological Sciences,
Journal Year:
2025,
Volume and Issue:
21(3), P. 958 - 973
Published: Jan. 6, 2025
Viral
mimicry
refers
to
an
active
antiviral
response
triggered
by
the
activation
of
endogenous
retroviruses
(ERVs),
usually
manifested
formation
double-stranded
RNA
(dsRNA)
and
cellular
interferon
response,
which
activates
immune
system
produces
anti-tumor
effects.
Epigenetic
studies
have
shown
that
epigenetic
modifications
(e.g.
DNA
methylation,
histone
modifications,
etc.)
play
a
crucial
role
in
tumorigenesis,
progression,
treatment
resistance.
Particularly,
alterations
methylation
may
be
closely
associated
with
suppression
ERVs
expression,
demethylation
restore
activity
thus
strengthen
tumor
response.
Therefore,
we
propose
viral
can
induce
responses
microenvironment
activating
expression
ERVs,
key
regulatory
this
process.
In
paper,
review
intersection
mimicry,
epigenetics
immunotherapy,
explore
possible
interactions
synergistic
effects
among
three,
aiming
provide
new
theoretical
basis
potential
strategies
for
cancer
immunotherapy.
Autoimmunity Reviews,
Journal Year:
2025,
Volume and Issue:
24(6), P. 103784 - 103784
Published: March 3, 2025
Autoimmune
diseases
result
from
complex
interactions
between
genetic
and
environmental
factors.
Recent
advances
in
epigenetic
research
shed
light
on
the
intricate
regulatory
mechanisms
that
contribute
to
development
progression
of
such
conditions.
The
present
review
aims
explore
role
modifications,
including
DNA
methylation,
histone
non-coding
RNAs,
context
autoimmune
diseases.
We
discuss
current
understanding
alterations
associated
with
various
disorders,
their
impact
immune
cell
function,
potential
as
innovative
therapeutic
targets.
Additionally,
we
highlight
main
future
directions
field
epigenetics
autoimmunity.
Molecular Cancer,
Journal Year:
2025,
Volume and Issue:
24(1)
Published: March 8, 2025
Epigenomic
modifications—such
as
DNA
methylation,
histone
acetylation,
and
methylation—and
their
implications
in
tumorigenesis,
progression,
treatment
have
emerged
a
pivotal
field
cancer
research.
Tumors
undergo
metabolic
reprogramming
to
sustain
proliferation
metastasis
nutrient-deficient
conditions,
while
suppressing
anti-tumor
immunity
the
tumor
microenvironment
(TME).
Concurrently,
immune
cells
within
immunosuppressive
TME
adaptations,
leading
alterations
function.
The
complicated
interplay
between
metabolites
epigenomic
modulation
has
spotlighted
significance
of
regulation
immunometabolism.
In
this
review,
characteristics
modification
associated
with
tumors
are
systematically
summarized
alongside
regulatory
roles
Classical
emerging
approaches
delineated
broaden
boundaries
research
on
crosstalk
immunometabolism
epigenomics.
Furthermore,
we
discuss
potential
therapeutic
strategies
that
target
modulate
modifications,
highlighting
burgeoning
synergy
therapies
immunotherapy
promising
avenue
for
treatment.
Bioengineering,
Journal Year:
2025,
Volume and Issue:
12(4), P. 341 - 341
Published: March 26, 2025
Cancer
treatment
has
historically
depended
on
conventional
methods
like
chemotherapy,
radiation,
and
surgery;
however,
these
strategies
frequently
present
considerable
limitations,
including
toxicity,
resistance,
negative
impacts
healthy
tissues.
In
addressing
challenges,
drug-free
cancer
therapies
have
developed
as
viable
alternatives,
utilizing
advanced
physical
biological
to
specifically
target
tumor
cells
while
reducing
damage
normal
This
review
examines
several
strategies,
such
high-intensity
focused
energy
beams,
nanosecond
pulsed
electric
fields,
photothermal
therapy
well
the
use
of
inorganic
nanoparticles
promote
selective
apoptosis.
We
also
investigate
significance
targeting
microenvironment,
precision
medicine,
immunotherapy
in
progression
personalized
therapies.
Although
approaches
demonstrate
significant
promise,
challenges
scalability,
safety,
regulatory
obstacles
must
be
resolved
for
clinical
application.
paper
presents
an
overview
current
research
therapies,
emphasizing
recent
advancements,
underlying
scientific
principles,
steps
required
implementation.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 2, 2025
Abstract
Extrachromosomal
DNA
(ecDNA)
is
a
prevalent
driver
of
cancer,
whose
random
segregation
promotes
aggressive
tumors.
Acentric
ecDNAs
attach
to
chromosomes
during
mitosis
for
segregation.
However,
the
molecular
mechanism
governing
ecDNA-chromosome
mitotic
interactions
remains
poorly
understood.
This
study
shows
that
histone
3
lysine
27
acetylation
(H3K27ac)-marked
chromatin
mitosis.
H3K27ac
depletion
resulted
in
ecDNA
detachment
from
chromosomes.
Diverse
bromodomain
proteins,
which
are
known
readers
H3K27ac,
stabilize
ecDNAs’
interaction,
exhibiting
context-dependent
and
mutually
complementary
roles.
Furthermore,
disruptions
Mediator
complex
RNA
polymerase
II
transcription
activity
both
dissociate
chromosomes,
suggesting
machinery
mediates
Mis-segregated
were
expelled
into
cytosol
degraded,
leading
diminished
oncogene
expression
reversal
therapy
resistance.
Our
research
provides
new
insights
interplay
between
acentric
inheritance
offering
novel
avenue
disrupting
ecDNA-driven
oncogenesis.
Biomolecules,
Journal Year:
2025,
Volume and Issue:
15(1), P. 71 - 71
Published: Jan. 6, 2025
The
tumor
microenvironment
(TME)
plays
a
pivotal
role
in
neoplastic
initiation
and
progression.
Epigenetic
machinery,
governing
the
expression
of
core
oncogenes
suppressor
genes
transformed
cells,
significantly
contributes
to
development
at
both
primary
distant
sites.
Recent
studies
have
illuminated
how
epigenetic
mechanisms
integrate
external
cues
downstream
signals,
altering
phenotype
stromal
cells
immune
cells.
This
remolds
area
surrounding
ultimately
fostering
an
immunosuppressive
microenvironment.
Therefore,
correcting
TME
by
targeting
modifications
holds
substantial
promise
for
cancer
treatment.
review
synthesizes
recent
research
that
elucidates
impact
specific
regulations-ranging
from
DNA
methylation
histone
chromatin
remodeling-on
within
TME.
Notably,
we
highlight
their
functional
roles
either
promoting
or
restricting
We
also
discuss
potential
applications
agents
treatment,
envisaging
ability
normalize
ecosystem.
aims
assist
researchers
understanding
dynamic
interplay
between
epigenetics
TME,
paving
way
better
therapy.