Briefings in Bioinformatics,
Год журнала:
2024,
Номер
26(1)
Опубликована: Ноя. 22, 2024
Abstract
Aging
is
a
complex
and
heterogeneous
biological
process
at
cellular,
tissue,
individual
levels.
Despite
extensive
effort
in
scientific
research,
comprehensive
understanding
of
aging
mechanisms
remains
lacking.
This
study
analyzed
aging-related
gene
networks,
using
single-cell
RNA
sequencing
data
from
>15
000
cells.
We
constructed
correlation
network,
integrating
expressions
into
the
weights
network
edges,
ranked
importance
random
walk
model
to
generate
matrix.
unsupervised
method
improved
clustering
performance
cell
types.
To
further
quantify
complexity
networks
during
aging,
we
introduced
structural
entropy.
The
findings
our
reveal
that
overall
entropy
increases
aged
cells
compared
young
However,
changes
varied
greatly
within
different
subtypes.
Specifically,
among
various
types
may
increase,
remain
unchanged,
or
decrease.
wide
range
be
closely
related
their
functions,
highlighting
cellular
heterogeneity
potential
key
reconfigurations.
Analyzing
provides
insights
molecular
behind
aging.
offers
new
evidence
theoretical
support
for
functions
Stem Cell Research & Therapy,
Год журнала:
2024,
Номер
15(1)
Опубликована: Июль 6, 2024
Abstract
Background
Dysfunction
or
deficiency
of
corneal
epithelium
results
in
vision
impairment
blindness
severe
cases.
The
rapid
and
effective
regeneration
epithelial
cells
relies
on
the
limbal
stem
(LSCs).
However,
molecular
functional
responses
LSCs
their
niche
to
injury
remain
elusive.
Methods
Single-cell
RNA
sequencing
was
performed
tissues
from
normal
mice
defect
models.
Bioinformatics
analysis
confirm
distinct
characteristics
cell
fates
LSCs.
Knockdown
Creb5
OSM
treatment
experiment
were
determine
roles
wound
healing.
Results
Our
data
defined
signatures
reconstructed
pseudotime
trajectory
cells.
Gene
network
analyses
characterized
transcriptional
landmarks
that
potentially
regulate
LSC
dynamics,
identified
a
transcription
factor
Creb5,
expressed
significantly
upregulated
after
injury.
Loss-of-function
experiments
revealed
silencing
delayed
healing
mobilization.
Through
cell–cell
communication
analysis,
we
609
candidate
regeneration-associated
ligand-receptor
interaction
pairs
between
cells,
discovered
unique
subset
Arg1
+
macrophages
infiltrated
injury,
which
present
as
source
Oncostatin
M
(OSM),
an
IL-6
family
cytokine,
demonstrated
effectively
accelerate
Conclusions
This
research
provides
valuable
single-cell
resource
reference
for
discovery
mechanisms
potential
clinical
interventions
aimed
at
ocular
surface
reconstruction.
As
individuals
age,
cognitive
decline
becomes
more
prominent,
concomitant
with
an
elevated
susceptibility
to
neurodegenerative
diseases
and
dementia.
Additionally,
symptoms
of
chronic
neuropsychiatric
tend
worsen
age.
It
is
crucial
highlight
that
the
aging
process
does
not
affect
uniformly,
its
effects
can
vary,
even
within
same
person.
This
review
aims
summary
impact
healthy
on
human
brain,
focusing
variations
from
different
brain
regions
cell
types.
Depending
specific
regions,
exhibits
thinning,
volume
reduction,
regional
shrinkage,
disrupted
tissue
integrity,
decreased
complexity,
or
iron
accumulation
during
aging.
Moreover,
cells
exhibit
morphology
function
changes
Neurons
undergo
characterized
by
reduced
dendrites,
dendritic
spines,
axons
less
compact
myelin
sheaths,
leading
a
significant
loss
synapses.
Comparatively,
glia
often
transform
into
reactive
phenotype.
Current Opinion in Genetics & Development,
Год журнала:
2024,
Номер
87, С. 102231 - 102231
Опубликована: Июль 24, 2024
Regenerative
capacities
and
strategies
vary
dramatically
across
animals,
as
well
between
cell
types,
organs,
with
age.
In
recent
years,
high-throughput
single-cell
transcriptomics
other
profiling
technologies
have
been
applied
to
many
animal
models
gain
an
understanding
of
the
cellular
molecular
mechanisms
underlying
regeneration.
Here,
we
review
studies
regeneration
in
diverse
contexts
summarize
key
concepts
that
emerged.
The
immense
regenerative
capacity
some
invertebrates,
exemplified
by
planarians,
is
driven
mainly
differentiation
abundant
adult
pluripotent
stem
cells,
whereas
cases,
involves
reactivation
embryonic
or
developmental
gene-regulatory
networks
differentiated
types.
However,
also
differs
from
development
ways,
including
use
regeneration-specific
types
gene
regulatory
networks.
Biological
age,
which
reflects
the
physiological
state
of
an
individual,
offers
a
better
predictive
value
than
chronological
age
for
age-related
diseases
and
mortality.
Nonetheless,
determining
accurate
functional
features
biological
remains
challenging
due
to
multifactorial
nature
aging.
Here,
we
established
unique
mouse
cohort
comprising
1576
male
female
outbred
SWISS
mice
subjected
or
not
high-fat,
high-sucrose
diet
investigate
multiorgan/system
aging
throughout
adulthood.
Comprehensive
phenotyping
at
ages
6,
12,
18,
24
months
revealed
notable
sex-specific
disparities
in
longitudinal
locomotion
patterns
multifunctional
parameters.
Topological
data
analysis
enabled
identification
functionally
similar
clusters
irrespective
age.
Moreover,
our
study
pinpointed
critical
markers
such
as
muscle
function,
anxiety
characteristics,
urinary
patterns,
reticulocyte
maturation,
cardiac
remodeling
metabolic
alterations,
underscoring
function
early
indicator
mice.
Briefings in Bioinformatics,
Год журнала:
2024,
Номер
26(1)
Опубликована: Ноя. 22, 2024
Abstract
Aging
is
a
complex
and
heterogeneous
biological
process
at
cellular,
tissue,
individual
levels.
Despite
extensive
effort
in
scientific
research,
comprehensive
understanding
of
aging
mechanisms
remains
lacking.
This
study
analyzed
aging-related
gene
networks,
using
single-cell
RNA
sequencing
data
from
>15
000
cells.
We
constructed
correlation
network,
integrating
expressions
into
the
weights
network
edges,
ranked
importance
random
walk
model
to
generate
matrix.
unsupervised
method
improved
clustering
performance
cell
types.
To
further
quantify
complexity
networks
during
aging,
we
introduced
structural
entropy.
The
findings
our
reveal
that
overall
entropy
increases
aged
cells
compared
young
However,
changes
varied
greatly
within
different
subtypes.
Specifically,
among
various
types
may
increase,
remain
unchanged,
or
decrease.
wide
range
be
closely
related
their
functions,
highlighting
cellular
heterogeneity
potential
key
reconfigurations.
Analyzing
provides
insights
molecular
behind
aging.
offers
new
evidence
theoretical
support
for
functions
