bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 16, 2024
ABSTRACT
The
ECM
is
a
complex
and
dynamic
meshwork
of
proteins
that
forms
the
framework
all
multicellular
organisms.
Protein
interactions
within
are
critical
to
building
remodeling
meshwork,
while
between
cell
surface
receptors
essential
for
initiation
signal
transduction
orchestration
cellular
behaviors.
Here,
we
report
development
MatriCom,
web
application
(
https://matrinet.shinyapps.io/matricom
)
companion
R
package
https://github.com/Izzilab/MatriCom
),
devised
mine
scRNA-Seq
datasets
infer
communications
components
different
populations
ECM.
To
impute
from
expression
data,
MatriCom
relies
on
unique
database,
MatriComDB,
includes
over
25,000
curated
involving
matrisome
components,
with
data
80%
∼1,000
genes
compose
mammalian
matrisome.
offers
option
query
open-access
sourced
large
sequencing
efforts
(Tabula
Sapiens,
Human
Atlas,
HuBMAP)
or
process
user-generated
datasets.
also
tailored
account
specific
rules
governing
protein
options
customize
output
through
stringency
filters.
We
illustrate
usability
example
human
kidney
communication
network.
Last,
demonstrate
how
integration
46
led
identification
both
ubiquitous
tissue-specific
patterns.
envision
will
become
powerful
resource
elucidate
roles
in
ECM-ECM
cell-ECM
their
dysregulations
context
diseases
such
as
cancer
fibrosis.
ONE
SENTENCE
SUMMARY
scRNA
systems
diverse
constitute
any
tissue
organ.
Frontiers in Cell and Developmental Biology,
Год журнала:
2024,
Номер
12
Опубликована: Март 1, 2024
The
extracellular
matrix
(ECM)
is
a
highly
complex
structure
through
which
biochemical
and
mechanical
signals
are
transmitted.
In
processes
of
cell
migration,
the
ECM
also
acts
as
scaffold,
providing
structural
support
to
cells
well
points
potential
attachment.
Although
well-studied
structure,
its
role
in
many
biological
remains
difficult
investigate
comprehensively
due
complexity
variation
within
an
organism.
tandem
with
experiments,
mathematical
models
helpful
refining
testing
hypotheses,
generating
predictions,
exploring
conditions
outside
scope
experiments.
Such
can
be
combined
calibrated
vivo
vitro
data
identify
critical
cell-ECM
interactions
that
drive
developmental
homeostatic
processes,
or
progression
diseases.
this
review,
we
focus
on
computational
such
migration
including
cancer
metastasis,
tissue
morphogenesis.
By
highlighting
predictive
power
these
models,
aim
help
bridge
gap
between
experimental
approaches
studying
provide
guidance
selecting
appropriate
model
framework
complement
corresponding
studies.
Frontiers in Network Physiology,
Год журнала:
2024,
Номер
4
Опубликована: Май 22, 2024
Pulmonary
fibrosis
is
a
deadly
disease
that
involves
the
dysregulation
of
fibroblasts
and
myofibroblasts,
which
are
mechanosensitive.
Previous
computational
models
have
succeeded
in
modeling
stiffness-mediated
behaviors;
however,
these
neglected
to
consider
stretch-mediated
behaviors,
especially
stretch-sensitive
channels
release
latent
TGF-β.
Here,
we
develop
explore
an
agent-based
model
spring
network
hybrid
capable
recapitulating
both
stiffness
stretch.
Using
model,
evaluate
role
mechanical
signaling
homeostasis
progression
during
self-healing
fibrosis,
respectively.
We
such
there
fibrotic
threshold
near
tends
towards
instability
or
below
heal.
The
healing
response
due
stretch
signal,
whereas
occurs
when
signal
overpowers
creating
positive
feedback
loop.
also
find
by
changing
proportional
weights
signals,
observe
heterogeneity
pathological
structure
similar
seen
human
IPF
tissue.
system
shows
emergent
behavior
bifurcations:
whether
will
heal
turn
depends
on
initial
organization
damage,
clearly
demonstrating
structure’s
pivotal
overall
network.
In
summary,
results
strongly
suggest
present
lungs
combined
with
effects
contribute
progression.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Май 11, 2024
ABSTRACT
The
plasticity
of
cancer
cells
allows
them
to
switch
between
different
migration
modes,
promoting
their
invasion
into
the
extracellular
matrix
(ECM)
and
hence
increasing
risks
metastasis.
Epithelial-to-mesenchymal
transitions
(EMT)
unjamming
provide
two
distinct
pathways
for
become
invasive,
but
it
is
still
unclear
what
extent
these
are
connected.
Here
we
addressed
this
question
by
performing
3D
spheroid
assays
lung
adenocarcinoma
(A549,
epithelial)
melanoma
(MV3,
mesenchymal-like)
cell
lines
in
collagen-based
hydrogels,
where
varied
both
invasive
character
(using
Transforming
Growth
Factor
(TGF)-
β
promote
EMT
metalloprotease
(MMP)
inhibition
block
cell-mediated
degradation)
porosity
matrix.
Using
a
quantitative
image
analysis
method
track
invasion,
discovered
that
onset
time
mostly
depended
on
corresponded
with
vimentin
levels,
while
subsequent
expansion
rate
MMP1
levels
thus
cell-matrix
interaction.
Morphological
revealed
spheroids
displayed
solid-like
(non-invasive)
behavior
small-pore
hydrogels
switched
fluid-like
(strand-based)
or
gas-like
(disseminating
cells)
phases
large-pore
when
were
more
mesenchymal-like.
Our
findings
consistent
as
function
motility
confinement
predicted
recent
models
show
coupled
via
EMT-dependent
degradation.
Regenerative Biomaterials,
Год журнала:
2024,
Номер
11
Опубликована: Янв. 1, 2024
Following
peripheral
nerve
anastomosis,
the
anastomotic
site
is
prone
to
adhesions
with
surrounding
tissues,
consequently
impacting
effectiveness
of
repair.
This
study
explores
development
and
efficacy
a
decellularized
epineurium
as
an
anti-adhesive
biofilm
in
Firstly,
entire
was
extracted
from
fresh
porcine
sciatic
nerves,
followed
by
decellularization
process.
The
efficiency
then
thoroughly
assessed.
Subsequently,
underwent
proteomic
analysis
determine
remaining
bioactive
components.
To
ensure
biosafety,
cytotoxicity
assays,
hemolysis
tests,
cell
affinity
assessments
immune
response
following
subcutaneous
implantation.
Finally,
functionality
determined
using
transection
anastomosis
model
rats.
result
indicated
that
process
effectively
removed
cellular
components
while
preserving
number
molecules,
this
effective
preventing
adhesion
promoting
repairment
functional
recovery.
In
conclusion,
represents
novel
promising
anti-adhesion
for
enhancing
surgical
outcomes
Journal of Molecular Pathology,
Год журнала:
2024,
Номер
5(4), С. 437 - 453
Опубликована: Окт. 5, 2024
The
extracellular
matrix
is
an
organized
three-dimensional
network
of
protein-based
molecules
and
other
macromolecules
that
provide
structural
biochemical
support
to
tissues.
Depending
on
its
properties,
the
influences
cell
adhesion
signal
transduction
and,
in
general,
can
influence
differentiation
proliferation
through
specific
mechanisms
chemical
mechanical
sensing.
development
body
tissues
during
ontogenesis
accompanied
by
changes
not
only
cells
but
also
composition
properties
matrix.
Similarly,
tumor
carcinogenesis
a
continuous
change
cells,
called
‘oncomatrix’,
as
matures,
from
primary
focus
stage
metastasis.
In
this
paper,
characteristics
are
considered,
well
evolution
patterns
be
used
biomarkers
oncological
diseases
potential
targets
for
promising
anti-tumor
therapies.
