bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Dec. 23, 2024
Abstract
Understanding
the
phenotypic
transitions
of
cancer
cells
is
crucial
for
elucidating
tumor
progression
mechanisms,
particularly
transition
from
a
non-invasive
spheroid
phenotype
to
an
invasive
network
phenotype.
We
developed
agent-based
model
(ABM)
using
Compucell3D,
open-source
biological
simulation
software,
investigate
how
varying
biophysical
and
biochemical
parameters
influence
emerging
properties
cellular
communities,
including
cell
growth,
division,
migration.
Our
focus
was
on
cell-cell
contact
adhesion
matrix
remodeling
effects
simplified
enzymatic
extracellular
subsequent
enhancements
chemotaxis
or
durotaxis
as
combined
effect
localized
secretion
chemoattractant.
By
chemoattractant
rate
energy,
we
simulated
their
behavior
driving
The
serves
digital
twin
3D
culture,
simulating
invasion
over
1
week,
validated
against
published
data.
simulations
track
emergent
morphological
collective
changes
key
metrics
such
circularity
invasion.
findings
indicate
that
increased
enhances
invasiveness
cells,
promoting
Additionally,
changing
energy
strong
weak
affects
compactness
spheroids,
resulting
in
lower
work
advances
understanding
by
providing
insights
into
mechanisms
behind
transitions.
Cells,
Journal Year:
2024,
Volume and Issue:
13(12), P. 1054 - 1054
Published: June 18, 2024
Over
the
past
decade,
development
of
three-dimensional
(3D)
models
has
increased
exponentially,
facilitating
unravelling
fundamental
and
essential
cellular
mechanisms
by
which
cells
communicate
with
each
other,
assemble
into
tissues
organs
respond
to
biochemical
biophysical
stimuli
under
both
physiological
pathological
conditions.
This
section
presents
a
concise
overview
most
recent
updates
on
significant
contribution
different
types
3D
cell
cultures
including
spheroids,
organoids
organ-on-chip
bio-printed
in
advancing
our
understanding
molecular
mechanisms.
The
case
studies
presented
include
breast
cancer
(BC),
endometriosis,
liver
microenvironment
infections.
In
BC,
establishment
culture
permitted
visualization
role
cancer-associated
fibroblasts
delivery
exosomes,
as
well
significance
physical
properties
extracellular
matrix
promoting
proliferation
invasion.
approach
also
become
valuable
tool
gaining
insight
general
specific
drug
resistance.
Given
considerable
heterogeneity
offer
more
accurate
representation
vivo
microenvironment,
thereby
identification
translation
novel
targeted
therapeutic
strategies.
advantages
provided
hepatic
environment,
conjunction
high
throughput
characterizing
various
platforms,
have
enabled
elucidation
complex
underlying
threatening
diseases.
A
limited
number
for
gut
skin
infections
been
developed.
However,
profound
comprehension
spatial
temporal
interactions
between
microbes,
host
their
environment
may
facilitate
advancement
vitro,
ex
disease
models.
Additionally,
it
pave
way
approaches
diverse
research
fields.
interested
reader
will
find
concluding
remarks
challenges
prospects
using
discovering
areas
covered
this
review.
Materials Today Bio,
Journal Year:
2025,
Volume and Issue:
31, P. 101640 - 101640
Published: March 4, 2025
The
progression
of
breast
cancer
is
influenced
by
the
stiffness
extracellular
matrix
(ECM),
which
becomes
stiffer
as
advances
due
to
increased
collagen
IV
and
laminin
secretion
cancer-associated
fibroblasts.
Intriguingly,
cells
cultivated
in
two-dimensions
exhibit
a
less
aggressive
behavior
when
exposed
weightlessness,
or
microgravity
conditions.
This
study
aims
elucidate
interplay
between
on
progression.
For
this
purpose,
three-dimensional
spheroids
cell
lines
(MCF-7
MDA-MB-231)
were
formed.
These
subsequently
bioprinted
hydrogels
varying
stiffness,
obtained
mixing
gelatin
methacrylate
poly(ethylene)
glycol
diacrylate
mixed
at
different
ratios.
constructs
printed
with
custom
stereolithography
(SLA)
bioprinter
converted
from
low-cost,
commercially
available
3D
printer.
structures,
encapsulating
spheroids,
then
placed
clinostat
(microgravity
simulation
device)
for
duration
seven
days.
Comparative
analyses
conducted
objects
cultured
under
standard
earth
gravity
Protein
expression
was
characterized
through
fluorescent
microscopy,
while
gene
MCF-7
analyzed
via
RNA
sequencing.
Remarkably,
influence
ECM
protein
levels
could
be
modulated
sometimes
even
reversed
study's
findings
hold
implications
refining
therapeutic
strategies
advanced
stages
-
an
array
genes
involved
reversing
metastatic
might
lead
discovery
new
compounds
that
used
clinical
setting.
APL Bioengineering,
Journal Year:
2025,
Volume and Issue:
9(1)
Published: March 1, 2025
Pancreatic
ductal
adenocarcinoma
(PDAC)
is
characterized
by
an
abundant
tumor-associated
stroma
composed
from
pancreatic
stellate
cells,
which
play
a
critical
role
in
tumor
progression.
Developing
accurate
vitro
models
requires
understanding
the
complex
interactions
between
cells
and
their
microenvironment.
In
this
study,
we
present
quantitative
imaging-based
characterization
of
three
dimensional
(3D)
self-organization
PDAC
tumour
spheroids
using
microfluidic
platform
that
mimics
key
aspects
Our
model
incorporates
collagen
type
I
hydrogels
to
recreate
extracellular
matrix,
activated
human
(HPSCs),
various
cell
types.
Advanced
imaging
techniques,
including
Lattice
Lightsheet
Microscopy,
allowed
us
analyze
3D
growth
spatial
organization
spheroids,
revealing
intricate
biomechanical
interactions.
results
indicate
alterations
matrix
properties-such
as
stiffness,
pore
size,
hydraulic
permeability-due
variations
concentration
significantly
influence
patterns
depending
on
subtype
epithelial-mesenchymal
phenotype.
Higher
concentrations
promoted
larger
epithelial-like
lines,
while
mesenchymal-type
required
increased
for
into
smaller
spheroids.
Furthermore,
coculture
with
HPSCs
affected
spheroid
formation
distinctly
based
each
line's
genetic
phenotypic
traits.
had
opposing
effects
lines:
one
line
exhibited
enhanced
growth,
another
showed
inhibited
formation,
whereas
mesenchymal-like
minimal
impact.
These
provide
insights
tumor-stroma
interactions,
emphasizing
importance
cell-specific
matrix-dependent
factors
advancing
our
progression
informing
future
therapeutic
strategies.
Frontiers in Bioengineering and Biotechnology,
Journal Year:
2025,
Volume and Issue:
13
Published: April 9, 2025
Metastasis,
the
leading
cause
of
death
in
cancer
patients,
arises
when
cells
disseminate
from
a
primary
solid
tumour
to
distant
organs.
Growth
and
invasion
often
involve
collective
cell
migration,
which
is
profoundly
influenced
by
cell-cell
interactions
extracellular
matrix
(ECM).
The
ECM's
biochemical
composition
mechanical
properties,
such
as
stiffness,
regulate
behaviour
migration
dynamics.
Mathematical
modelling
serves
pivotal
tool
for
studying
predicting
these
complex
dynamics,
with
hybrid
discrete-continuous
models
offering
powerful
approach
combining
agent-based
representations
continuum
descriptions
surrounding
microenvironment.
In
this
study,
we
investigate
impact
ECM
modulated
via
ribose-induced
collagen
cross-linking,
on
spheroid
growth
invasion.
We
employed
model
implemented
PhysiCell
simulate
successfully
replicating
three-dimensional
vitro
experiments.
incorporates
detailed
cell-ECM
interactions,
remodelling,
proliferation.
Our
simulations
align
experimental
observations
two
breast
lines,
non-invasive
MCF7
invasive
HCC
1954,
under
varying
stiffness
conditions.
results
demonstrate
that
increased
due
cross-linking
inhibits
cells,
whereas
remain
largely
unaffected.
Furthermore,
our
show
higher
degradation
not
only
enables
but
also
facilitates
formation
multicellular
protrusions.
Conversely,
increasing
maximum
speed
can
reach
enhances
while
promoting
single-cell
This
understanding
interplay
between
proliferation,
paving
way
future
studies
incorporating
additional
characteristics
microenvironmental
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 23, 2025
Abstract
Basement
membrane,
the
specialized
extracellular
matrix
(ECM)
that
compartmentalizes
endothelial
and
epithelial
cells,
is
final
frontier
in
bioengineering.
The
fibrillar
collagens
(Col
I
Col
III)
of
interstitial
are
commonly
used
for
tissue
modeling,
but
networking
scaffold
basement
membrane
(human
IV
VI)
remain
elusive.
Commercial
hydrogels
like
Matrigel
simulate
ill-defined,
dilute,
variable
contain
murine
proteins.
Here,
we
investigated
whether
human
mesenchymal
stromal
cells
(MSCs)
could
be
to
produce
3D
scaffolds
amenable
decellularization
downstream
applications
Using
a
xeno-free,
process,
MSCs
from
placenta,
umbilical
cord,
bone
marrow
adipose
tissues
were
cultivated
as
adherent
multilayers
or
free-floating
spheroids.
Matrix
assembly
was
assessed
daily
by
fluorescence
imaging
western
blot,
revealing
de
novo,
systematic,
development.
Notably,
these
rich
membrane-specific
components
VI.
Interestingly,
observed
distinct
combinations
alpha
chains
other
depending
on
their
origin.
Ongoing
work
aims
combine
this
intrinsic
patterning
with
strategic
process
parameters
refine
composition
resemble
target
tissues,
develop
assays
processes
angiogenesis
incorporate
relevant
biology
readout.
Current Opinion in Cell Biology,
Journal Year:
2024,
Volume and Issue:
90, P. 102422 - 102422
Published: Aug. 30, 2024
Many
solid
tumors
exhibit
significant
genetic,
cellular,
and
biophysical
heterogeneity
which
dynamically
evolves
during
disease
progression
after
treatment.
This
constant
flux
in
cell
composition,
phenotype,
spatial
relationships,
tissue
properties
poses
challenges
accurately
diagnosing
treating
patients.
Much
of
the
complexity
lies
unraveling
molecular
changes
different
tumor
compartments,
how
they
influence
one
another
space
time
where
vulnerabilities
exist
that
might
be
appropriate
to
target
therapeutically.
Recent
advances
profiling
tools
technologies
are
enabling
new
insight
into
underlying
biology
complex
tumors,
creating
a
greater
understanding
intricate
relationship
between
types,
states,
microenvironment.
Here
we
reflect
on
some
recent
discoveries
this
area,
key
knowledge
technology
gaps
lie,
advancements
measurements
vitro
models
for
study
intratumoral
heterogeneity.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: March 29, 2024
Abstract
Spheroids
have
become
principal
three-dimensional
biological
models
to
study
cancer,
developmental
processes,
and
drug
efficacy.
For
spheroid
generation,
ultra-low
attachment
plates
are
noteworthy
due
their
simplicity,
compatibility
with
automation,
experimental
commercial
accessibility.
Nonetheless,
it
is
unknown
whether
what
degree
the
plate
type
impacts
formation
biology.
This
employed
automated
brightfield
microscopy
systematically
compare
size
eccentricity
of
spheroids
formed
in
six
different
types
using
four
distinct
human
cell
lines,
i.e.,
CCD-1137Sk
fibroblasts,
HaCaT
keratinocytes,
MDA-MB-231
HT-29
cancer
cells.
Results
showed
that
all
exhibited
similar
sphe-roid-forming
capabilities,
gross
patterns
growth
or
shrinkage
during
days
after
seeding
were
comparable.
Yet,
varied
among
specific
lines
types.
A
confocal
wholemount
analysis
by
a
novel
pipeline
AI-based
3D-image
procedures
revealed
changes
proliferation,
number,
nuclear
volume,
keratino-cyte
differentiation,
which
accompanied
altered
YAP1-signals.
The
findings
show
may
influence
outcome
campaigns.
It
advisable
scan
for
optimal
configuration
investigation
instead
one
standard
kinds
applications.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: June 12, 2024
We
implemented
a
multimodal
set
of
functional
imaging
techniques
optimized
for
deep-tissue
to
investigate
how
cancer
cells
invade
surrounding
tissues
and
their
physiological
properties
change
in
the
process.
As
model
invasion
extracellular
matrix,
we
created
3D
spheroids
from
triple-negative
breast
(MDA-MB-231)
non-tumorigenic
epithelial
(MCF-10A).
analyzed
multiple
hallmarks
within
same
spheroid
by
combining
number
techniques,
such
as
metabolic
NADH
Fluorescence
Lifetime
Imaging
Microscopy
(NADH-FLIM),
hyperspectral
solvatochromic
lipophilic
dye
(Nile
Red)
matrix
Second
Harmonic
Generation
(SHG).
included
phasor-based
bioimage
analysis
at
three
different
time
points,
tracking
both
morphological
biological
properties,
including
cellular
metabolism,
fatty
acids
storage,
collagen
organization.
Employing
this
deep-imaging
framework,
observed
quantified
cell
plasticity
response
changes
environment
composition.
Biomedical Optics Express,
Journal Year:
2024,
Volume and Issue:
15(9), P. 5199 - 5199
Published: Aug. 6, 2024
Confocal
frequency-domain
fluorescence
lifetime
and
Förster
resonance
energy
transfer
(FRET)
microscopy
of
Chinese
hamster
ovary
(CHO-K1)
cells
expressing
the
vinculin
tension
sensor
(VinTS)
is
used
to
compare
in
three-dimensional
(3D)
multicellular
aggregates
2D
cellular
monolayers.
In
both
3D
cultures,
FRET
efficiency
VinTS
5-6%
lower
than
that
VinTL
(p
<
0.05),
a
tail-less
control
which
cannot
bind
actin
or
paxillin.
The
difference
between
can
be
mitigated
by
treatment
with
Rho-associated
kinase
inhibitor
Y-27632,
demonstrating
under
cultures.
However,
there
an
overall
decrease
compared
Expression
cultures
exhibits
puncta
consistent
adhesions.
While
paxillin
present
at
sites
expression
monolayers,
it
generally
absent
from
aggregates.
results
suggest
experiences
modified
environment
monolayers
provide
basis
for
further
investigation
molecular
sensors
tissue
models.