DeXtrusion: automatic recognition of epithelial cell extrusion through machine learning in vivo
Development,
Journal Year:
2023,
Volume and Issue:
150(13)
Published: June 7, 2023
ABSTRACT
Accurately
counting
and
localising
cellular
events
from
movies
is
an
important
bottleneck
of
high-content
tissue/embryo
live
imaging.
Here,
we
propose
a
new
methodology
based
on
deep
learning
that
allows
automatic
detection
their
precise
xyt
localisation
fluorescent
imaging
without
segmentation.
We
focused
the
cell
extrusion,
expulsion
dying
cells
epithelial
layer,
devised
DeXtrusion:
pipeline
recurrent
neural
networks
for
extrusion/cell
death
in
large
epithelia
marked
with
contour.
The
pipeline,
initially
trained
Drosophila
pupal
notum
E-cadherin,
easily
trainable,
provides
fast
accurate
extrusion
predictions
range
conditions,
can
also
detect
other
events,
such
as
division
or
differentiation.
It
performs
well
tissues
reasonable
re-training.
Our
could
be
applied
detected
by
microscopy
help
to
democratise
use
event
detections
developing
tissues.
Language: Английский
Exploring caspase-dependent non-lethal cellular processes using Drosophila
Frontiers in Cell Death,
Journal Year:
2024,
Volume and Issue:
3
Published: Oct. 21, 2024
Caspases
are
cysteine
aspartic
acid
proteases
conserved
in
animals
that
not
only
execute
apoptosis,
but
also
regulate
diverse
cellular
processes
independent
of
which
termed
caspase-dependent
non-lethal
(CDPs).
Owing
to
its
strong
genetics
detect
and
manipulate
caspase
activity
cells
interest
vivo
,
Drosophila
melanogaster
serves
as
an
excellent
model
organism
for
analyzing
CDPs.
This
is
further
supported
by
the
fact
apoptotic
signaling,
well
CDPs
their
mechanisms,
are,
part,
other
animals.
Here,
we
present
a
review
guide
researchers
studying
using
.
In
this
review,
provide
overview
current
understanding
regulates
activation
available
genetic
tools
characteristics
detecting
manipulating
so
can
choose
appropriate
own
experimental
settings.
We
introduce
identified
including
brief
description
discovery
characterization
processes.
describe
underlying
molecular
mechanisms
several
well-characterized
CDPs,
regulatory
enable
activation.
Finally,
use
proximity
labeling
techniques,
especially
TurboID,
facilitates
analysis
mechanisms.
Because
caspases
various
functions,
no
longer
considered
point
return
cell
death.
Understanding
will
advance
our
states
living
dying
cells,
along
with
intermediate
states.
Language: Английский
Epithelial apoptosis: A back-and-forth mechanical interplay between the dying cell and its surroundings
Seminars in Cell and Developmental Biology,
Journal Year:
2025,
Volume and Issue:
168, P. 1 - 12
Published: Feb. 21, 2025
Language: Английский
Intestinal Tissue Mechanics Regulate Angiogenesis and Stem Cell Proliferation via Vascular Piezo
J. Phillips,
No information about this author
Jessica Perochon,
No information about this author
Cai T. Johnson
No information about this author
et al.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 16, 2025
Abstract
The
vasculature
is
a
prominent
component
of
developmental
and
adult
tissue
microenvironments.
How,
specific
characteristics
environmental
states
influence
vascular
biology
function,
remains
largely
understudied.
Previously,
we
discovered
crosstalk
between
the
intestinal
epithelium
vasculature-like
tracheal
system
fruit
fly
Drosophila
melanogaster
,
which
driven
by
reactive
oxygen
species
(ROS)
during
pathogen
induced-intestinal
regeneration.
However,
chemical
stress
signals
alone
are
insufficient
to
explain
rich
diversity
vasculature/tissue
interactions
in
living
systems
justify
widely
observed
adaptation
network
physiology
disease.
Here,
uncover
reciprocal,
mechanochemical
interorgan
communication
intestine
its
niche,
shapes
epithelial
adaptations
drives
stem
cell
proliferation
regeneration
tumour
growth.
Mechanistically,
apoptotic
cells
within
regenerating
induce
local
global
mechanical
changes
gut,
results
activation
upregulation
mechanosensitive
ion
channel
Piezo
subset
gut-associated
trachea.
molecular
program
trachea
through
transcription
factor
Yorkie/YAP,
leading
remodelling
proliferation.
Furthermore,
identify
non-redundant
role
Piezo1
driving
crypt
inducing
growth,
WNT
signalling
activity,
mouse
small
intestine.
Our
cross-species
vivo
study
reveals
previously
unrecognised
mechanosensory
regulation
tumourigenesis
vascular-stem
niche
highlights
importance
studying
context
understand
plasticity
complexity
tissue/vasculature
organ.
Language: Английский
Integration of past caspase activity biases cell elimination in vivo
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: May 20, 2025
Abstract
The
fine
tuning
of
apoptosis
in
epithelia
is
essential
for
regulating
tissue
size,
shape,
homeostasis
and
the
maintenance
sealing
properties.
Regulation
cell
death
mostly
orchestrated
by
activation
Caspases,
proteases
which
were
long
thought
to
trigger
an
irreversible
engagement
death.
However,
recent
data
vivo
vitro
outline
numerous
non-apoptotic
functions
caspases
as
well
quite
ubiquitous
sublethal
effector
during
development.
Yet,
it
remains
unclear
many
instances
what
drives
bifurcation
between
survival
upon
caspase
activation.
existence
a
activity
threshold
was
generally
considered
underpin
this
binary
decision,
but
never
assessed
quantitatively
especially
at
single
level.
Using
quantitative
live
imaging
combined
with
machine
learning
optogenetics
Drosophila
pupal
notum
(a
layer
epithelium),
we
reveal
first
time
large
heterogeneity
sensitivity
cells,
distinct
spatial
domains
low
or
high
caspases.
correlative
perturbative
experiments,
central
role
past
exposure
sensitises
cells
several
hours.
Integrating
information
about
sufficient
explain
most
global
pattern
predict
level
will
engage
apoptosis.
Finally,
demonstrate
that
subset
bias
elimination
clonal
level,
thus
revealing
alternative
mechanism
physiological
competition.
Altogether,
work
reveals
new
regulation
downstream
can
be
developmentally
regulated
selection
Language: Английский
Forward Engineering Organ Development and Cancer Therapeutics with Optogenetics
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: May 22, 2025
Robust
growth
control
is
an
essential
requirement
for
the
survival
of
living
organisms,
while
its
dysregulation
results
in
diseases
such
as
cancer.
However,
a
significant
knowledge
gap
exists
understanding
how
precise
organ
achieved.
The
growing
arsenal
optogenetic
toolkits
allows
precise,
noninvasive
cellular
signaling
vivo,
enabling
research
into
bioelectrical
and
chemical
cues
regulate
growth.
Here,
we
used
red-light-activated
channelrhodopsin,
CsChrimson,
to
stimulate
intracellular
calcium
dynamics
wing
epithelium
Drosophila
melanogaster
,
established
model
system
investigating
size
control.
By
varying
light
intensity
activation
systematically,
identified
biphasic
regulation
final
size.
Illumination
CsChrimson
depolarizes
cells
stimulates
spikes
cytosolic
concentrations,
phenomenon
explained
by
computational
that
incorporates
inclusion
both
junction
closure
voltage-gated
channel
activation.
This
tunes
downstream
effectors
involved
apoptosis.
In
particular,
found
prolonged
bright
red
exposure
(100
lux/12
hours)
increased
cell
death
imaginal
discs
caused
severe
morphological
abnormalities
adult
wings,
with
phenotypic
severity
dependent
on
stimulation
parameters
defined
illumination
period
Strikingly,
optimum
level
dim,
pulsatile
(5
lux,
1
minute
on/off
pulse
train)
resulted
overgrown
organs
significantly
upregulated
proliferation.
We
also
co-expressed
oncogene,
Ras
V12
showed
experimental
optical
simulation
can
be
exploited
morphology
tumorous
tissues
initiate
targeted
remission
Our
findings
approach
provide
powerful
framework
dissect
role
dynamic
physiological
events
organogenesis
offer
translational
insights
new
therapeutic
strategies
applications
cancer
regenerative
medicine.
Language: Английский
Organogenesis: Cell death matters in size and shape regulation
Current Biology,
Journal Year:
2024,
Volume and Issue:
34(2), P. R62 - R64
Published: Jan. 1, 2024
Language: Английский
Developmental delay ensures global tissue size robustness upon local induction of apoptosis
Ralitza Staneva,
No information about this author
Gabriel Sobczyk-Moran,
No information about this author
Florence Levillayer
No information about this author
et al.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Dec. 21, 2024
Abstract
The
capacity
of
our
tissues
to
cope
with
external
and
internal
stress
relies
on
the
tight
coupling
between
cell
proliferation,
growth
death.
This
is
assumed
be
based
compensatory
where
local
mitogenic
signals
mechanical
inputs
generated
by
dying
cells
promote
neighbouring
proliferation.
However,
proliferation
was
mostly
studied
in
context
massive
death
induction,
irradiation,
surgical
tissue
ablation
or
upon
genetic
perturbation
apoptosis
execution.
It
remains
thus
unclear
whether
same
mechanism
operates
during
physiological
programmed
mild
induction
apoptosis,
especially
vivo
.
Here,
we
use
Drosophila
prospective
wing
(the
larval
disc),
study
impact
size
pattern.
We
first
confirmed
that
could
recover
its
final
compensate
for
apoptosis.
using
spatial
statistics
found
surprisingly
not
associated
any
increase
it
clonal
compartment
Compensation
driven
instead
a
JNK
dependant
delay
lengthening
stage
which
required
reach
target
size.
These
results
suggest
compensation
here
global
response
rather
induction.
Accordingly,
while
total
maintained
despite
this
fails
correct
reduction
number,
hence
modulating
shape
proportion.
Overall,
opens
novel
perspectives
regulation
outlines
context-dependency
mechanisms.
Language: Английский