Biomacromolecules,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 29, 2025
The
field
of
mechanobiology
has
grown
in
the
past
decade,
but
limited
studies
investigate
how
extracellular
matrix
affects
cell
metabolome.
methionine
cycle
involves
catabolism
and
regeneration
through
donation
recovery
a
single
methyl
group;
this
group
can
methylate
DNA,
RNA,
proteins
to
alter
gene
expression
protein-protein
interactions.
Through
studying
cells
cultured
on
fibrous
(mimicking
healthy
matrice
(ECM))
flat
severely
fibrotic
ECM)
substrates,
we
observed
an
increase
enzyme
substrate.
We
also
present
is
modulated
by
ECM
transmembrane
protein
integrin
β1.
By
inhibiting
activation
ligand-mimicking
peptide
RGD,
that
was
protected
from
alteration.
results
presented
provide
insight
into
possible
therapeutic
targets
for
diseases
knowledge
mechanisms
which
alters
processes.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Март 12, 2024
Summary
Gene
expression
is
orchestrated
by
transcription
factors,
which
function
within
the
context
of
a
three-dimensional
genome.
Zinc
finger
protein
143
(ZNF143/ZFP143)
factor
that
has
been
implicated
in
both
gene
activation
and
chromatin
looping.
To
study
direct
consequences
ZNF143/ZFP143
loss,
we
generated
degron
line.
Our
results
show
depletion
no
effect
on
Systematic
analysis
occupancy
data
revealed
commonly
used
antibody
cross-reacts
with
CTCF,
leading
to
its
incorrect
association
loops.
Nevertheless,
specifically
activates
nuclear-encoded
mitochondrial
genes
loss
leads
severe
dysfunction.
Using
an
vitro
embryo
model,
find
essential
regulator
organismal
development.
establish
as
conserved
transcriptional
cell
proliferation
differentiation
safeguarding
activity.
Highlights
Acute
degradation
ZFP143
rapid
specific
transcription.
Molecular
are
inconsistent
role
proteins.
regulation
homeostasis
critical
for
multicellular
Graphical
Abstract
PLoS ONE,
Год журнала:
2025,
Номер
20(3), С. e0317309 - e0317309
Опубликована: Март 26, 2025
Aggregating
low
numbers
of
mouse
embryonic
stem
cells
(mESCs)
and
inducing
Wnt
signalling
generates
‘gastruloids’,
self-organising
complex
structures
that
display
an
anteroposterior
organisation
cell
types
derived
from
all
three
germ
layers.
Current
gastruloid
protocols
considerable
heterogeneity
between
experiments
in
terms
morphology,
elongation
efficiency,
type
composition.
We
therefore
investigated
whether
altering
the
mESC
pluripotency
state
would
provide
more
consistent
results.
By
growing
lines
two
different
genetic
backgrounds
intervals
ESLIF
2i
medium
was
modulated,
culture
as
well
resulting
gastruloids
were
analysed.
Microscopic
analysis
showed
a
pre-culture-specific
effect
on
formation,
aspect
ratio
reproducibility.
RNA-seq
start
population
confirmed
short-term
pulses
modulate
state,
result
cellular
states.
Since
multiple
epigenetic
regulators
detected
among
top
differentially
expressed
genes,
we
further
analysed
genome-wide
DNA
methylation
H3K27me3
distributions.
observed
differences
conditions,
most
dominantly
promoter
regions
developmental
regulators.
Lastly,
when
composition
grown
these
pre-cultures,
mESCs
subjected
to
2i-ESLIF
preceding
aggregation
generated
consistently,
including
mesodermal
contributions
compared
ESLIF-only
control.
These
results
indicate
optimisation
allows
modulation
differentiation
during
formation.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Сен. 23, 2023
During
early
development
of
multi-cellular
animals,
cells
self-organize
to
set
up
the
body
axes,
such
as
primary
head-to-tail
axis,
based
on
which
later
plan
is
defined.
Several
signaling
pathways
are
known
control
axis
formation.
Here,
we
show,
however,
that
also
tissue
mechanics
plays
an
important
role
during
this
process.
We
focus
emergence
a
in
initially
spherical
aggregates
mouse
embryonic
stem
cells,
mirrors
events
embryo.
These
break
rotational
symmetry
establish
axial
organization
with
domains
different
expression
profiles,
e.g.
transcription
factor
T/Bra
and
adhesion
molecule
E-cadherin.
Combining
quantitative
microscopy
physical
modeling,
identify
large-scale
flows
recirculation
component
demonstrate
they
significantly
contribute
breaking.
show
recirculating
explained
by
difference
surface
tension
across
domains,
akin
Marangoni
flows,
further
confirm
aggregate
fusion
experiments.
Our
work
highlights
formation
not
only
driven
biochemical
processes,
but
it
can
be
amplified
flows.
expect
type
amplification
may
operate
many
other
organoid
in-vivo
systems.
ABSTRACT
Many
developmental
processes
rely
on
the
localized
activation
of
receptor
tyrosine
kinases
and
their
canonical
downstream
effectors
Erk
Akt,
yet
specific
roles
played
by
each
these
signals
is
still
poorly
understood.
Gastruloids,
3D
cell
culture
models
mammalian
gastrulation
axial
elongation,
enable
quantitative
dissection
signaling
patterns
responses
in
a
simplified,
experimentally
accessible
context.
We
find
that
mouse
gastruloids
contain
posterior-to-anterior
gradients
Akt
phosphorylation
induced
distinct
kinases,
with
features
pattern
expression
its
target
Snail
exhibiting
hallmarks
size-invariant
scaling.
Both
contribute
to
proliferation,
whereas
also
sufficient
induce
precipitate
profound
tissue
shape
changes.
further
uncover
convert
entire
gastruloid
one
two
mesodermal
fates
depending
position
along
anteroposterior
axis.
In
all,
data
demonstrate
functional
for
core
development
suggest
how
modules
might
be
harnessed
engineer
user-defined
tissues
predictable
shapes
fates.
Cell stem cell,
Год журнала:
2024,
Номер
31(7), С. 1072 - 1090.e8
Опубликована: Май 15, 2024
Gastrulation
is
a
critical
stage
in
embryonic
development
during
which
the
germ
layers
are
established.
Advances
sequencing
technologies
led
to
identification
of
gene
regulatory
programs
that
control
emergence
and
their
derivatives.
However,
proteome-based
studies
early
mammalian
scarce.
To
overcome
this,
we
utilized
gastruloids
multilayered
mass
spectrometry-based
proteomics
approach
investigate
global
dynamics
(phospho)
protein
expression
gastruloid
differentiation.
Our
findings
revealed
many
proteins
with
temporal
unique
profiles
for
each
layer,
also
validated
using
single-cell
technology.
Additionally,
profiled
enhancer
interaction
landscapes
P300
proximity
labeling,
numerous
gastruloid-specific
transcription
factors
chromatin
remodelers.
Subsequent
degron-based
perturbations
combined
RNA
(scRNA-seq)
identified
role
ZEB2
mouse
human
somitogenesis.
Overall,
this
study
provides
rich
resource
developmental
synthetic
biology
communities
endeavoring
understand
embryogenesis.
Minimal
in
vitro
systems
composed
of
embryonic
stem
cells
(ESCs)
have
been
shown
to
recapitulate
the
establishment
anteroposterior
(AP)
axis.
In
contrast
native
embryo,
ESC
aggregates
-
such
as
gastruloids
can
break
symmetry,
which
is
demarcated
by
polarization
mesodermal
marker
T,
autonomously
without
any
localized
external
cues.
However,
associated
earliest
patterning
events,
spatial
restriction
cell
fates
and
concomitant
transcriptional
changes,
remain
poorly
understood.
Here,
we
dissect
dynamics
AP
axis
mouse
gastruloids,
particularly
before
Wnt
stimulation.
Through
single-cell
RNA
sequencing,
identify
key
state
transitions
molecular
signatures
T+
T-
populations
underpinning
polarization.
We
also
show
that
this
process
robust
modifications
aggregate
size.
Finally,
transcriptomic
comparison
with
embryo
indicates
develop
similar
mesendodermal
types,
despite
initial
differences
their
primed
pluripotent
populations,
adopt
a
more
mesenchymal
lieu
an
epiblast-like
transcriptome.
Hence,
our
findings
suggest
possibility
alternate
states
vivo
converge
onto
fates.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Июнь 5, 2023
Abstract
When
cultured
in
three
dimensional
spheroids,
mammalian
stem
cells
can
reproducibly
self-organize
a
single
anterior-posterior
axis
and
sequentially
differentiate
into
structures
resembling
the
primitive
streak
tailbud.
Whereas
embryo’s
body
axes
are
instructed
by
spatially
patterned
extra-embryonic
cues,
it
is
unknown
how
these
cell
gastruloids
break
symmetry
to
define
(A-P)
axis.
Here,
we
use
synthetic
gene
circuits
trace
early
intracellular
signals
predict
cells’
future
position
gastruloid.
We
show
that
Wnt
signaling
evolves
from
homogeneous
state
polarized
state,
identify
critical
6-hour
time
period
when
single-cell
activity
predicts
cellular
position,
prior
appearance
of
patterns
or
morphology.
Single-cell
RNA
sequencing
live-imaging
reveal
Wnt-high
Wnt-low
contribute
distinct
types
suggest
axial
breaking
driven
sorting
rearrangements
involving
differential
adhesion.
further
extend
our
approach
other
canonical
embryonic
pathways,
revealing
even
earlier
heterogeneity
TGFβ
A-P
modulates
during
period.
Our
study
reveals
sequence
dynamic
processes
transform
uniform
aggregate
structure
demonstrates
morphological
emerge
out
movements
absence
exogenous
patterning
cues.
Highlights
Symmetry-breaking
gastruloid
protocol
where
high
posterior
domain.
Synthetic
record
Wnt,
Nodal
BMP
with
resolution.
Heterogeneity
at
96
h
positions
types.
differences
influenced
Nodal/BMP
activity.
ABSTRACT
Primordial
germ
cells
(PGCs)
are
the
early
embryonic
precursors
of
gametes
–
sperm
and
egg
cells.
PGC-like
(PGCLCs)
can
currently
be
derived
in
vitro
from
pluripotent
exposed
to
signalling
cocktails
aggregated
into
large
bodies,
but
these
do
not
recapitulate
native
environment
during
PGC
formation.
Here,
we
show
that
mouse
gastruloids,
a
three-dimensional
model
gastrulation,
contain
population
gastruloid-derived
PGCLCs
(Gld-PGCLCs)
resemble
PGCs
vivo.
Importantly,
conserved
organisation
gastruloids
leads
coordinated
spatial
temporal
localisation
Gld-PGCLCs
relative
surrounding
somatic
cells,
even
absence
specific
exogenous
PGC-specific
or
extra-embryonic
tissues.
In
self-organised
interactions
between
tissues,
including
endodermal
epithelium,
enables
specification
subsequent
maturation
pool
Gld-PGCLCs.
As
such,
represent
new
source
and,
owing
their
inherent
co-development,
serve
as
novel
study
dynamics
development
within
integrated
tissue
environments.