bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Sept. 9, 2023
Amniogenesis
is
triggered
in
a
collection
of
pluripotent
epiblast
cells
as
the
human
embryo
implants.
To
gain
insights
into
critical
but
poorly
understood
transcriptional
machinery
governing
amnion
fate
determination,
we
examined
evolving
transcriptome
developing
stem
cell-derived
model
at
single
cell
level.
This
analysis
revealed
several
continuous
amniotic
progressing
states
with
state-specific
markers,
which
include
previously
unrecognized
CLDN10+
progenitor
state.
Strikingly,
found
that
expression
CLDN10
restricted
to
amnion-epiblast
boundary
region
post-implantation
sac
well
peri-gastrula
cynomolgus
macaque
embryo,
bolstering
growing
notion
that,
this
stage,
site
active
amniogenesis.
Bioinformatic
published
primate
sequencing
data
further
confirmed
expressed
amnion.
Additionally,
our
loss
function
shows
promotes
suppresses
primordial
germ
cell-like
fate.
Overall,
study
presents
comprehensive
amniogenic
transcriptomic
resource
and
identifies
population
peri-gastrula.
Cell,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 1, 2024
Quantifying
spatiotemporal
dynamics
during
embryogenesis
is
crucial
for
understanding
congenital
diseases.
We
developed
Spateo
(https://github.com/aristoteleo/spateo-release),
a
3D
modeling
framework,
and
applied
it
to
mouse
atlas
at
E9.5
E11.5,
capturing
eight
million
cells.
enables
scalable,
partial,
non-rigid
alignment,
multi-slice
refinement,
mesh
correction
create
molecular
holograms
of
whole
embryos.
It
introduces
digitization
methods
uncover
multi-level
biology
from
subcellular
organ,
identifying
expression
gradients
along
orthogonal
axes
emergent
structures,
e.g.,
secondary
organizers
such
as
midbrain-hindbrain
boundary
(MHB).
further
jointly
models
intercellular
intracellular
interaction
dissect
signaling
landscapes
in
including
the
zona
limitans
intrathalamica
(ZLI).
Lastly,
"morphometric
vector
fields"
cell
migration
integrates
spatial
differential
geometry
unveil
programs
underlying
asymmetrical
murine
heart
organogenesis
others,
bridging
macroscopic
changes
with
dynamics.
Thus,
study
organ
ecology
level
space
over
time.
Nature Methods,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 14, 2024
Stem
cell-based
embryo
models
offer
unprecedented
experimental
tools
for
studying
early
human
development.
The
usefulness
of
hinges
on
their
molecular,
cellular
and
structural
fidelities
to
in
vivo
counterparts.
To
authenticate
models,
single-cell
RNA
sequencing
has
been
utilized
unbiased
transcriptional
profiling.
However,
an
organized
integrated
RNA-sequencing
dataset,
serving
as
a
universal
reference
benchmarking
remains
unavailable.
Here
we
developed
such
through
the
integration
six
published
datasets
covering
development
from
zygote
gastrula.
Lineage
annotations
are
contrasted
validated
with
available
nonhuman
primate
datasets.
Using
stabilized
Uniform
Manifold
Approximation
Projection,
constructed
embryogenesis
prediction
tool,
where
query
can
be
projected
annotated
predicted
cell
identities.
this
examined
highlighting
risk
misannotation
when
relevant
references
not
authentication.
Small Methods,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 18, 2025
Abstract
Rapidly
developing
spatial
omics
technologies
provide
us
with
new
approaches
to
deeply
understanding
the
diversity
and
functions
of
cell
types
within
organisms.
Unlike
traditional
approaches,
enable
researchers
dissect
complex
relationships
between
tissue
structure
function
at
cellular
or
even
subcellular
level.
The
application
provides
perspectives
on
key
biological
processes
such
as
nervous
system
development,
organ
tumor
microenvironment.
This
review
focuses
advancements
strategies
technologies,
summarizes
their
applications
in
biomedical
research,
highlights
power
advancing
life
sciences
related
development
disease.
Nature,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 19, 2025
Depicting
spatial
distributions
of
disease-relevant
cells
is
crucial
for
understanding
disease
pathology1,2.
Here
we
present
genetically
informed
mapping
complex
traits
(gsMap),
a
method
that
integrates
transcriptomics
data
with
summary
statistics
from
genome-wide
association
studies
to
map
human
traits,
including
diseases,
in
spatially
resolved
manner.
Using
embryonic
datasets
covering
25
organs,
benchmarked
gsMap
through
simulation
and
by
corroborating
known
trait-associated
or
regions
various
organs.
Applying
brain
data,
reveal
the
distribution
glutamatergic
neurons
associated
schizophrenia
more
closely
resembles
cognitive
than
mood
such
as
depression.
The
schizophrenia-associated
were
distributed
near
dorsal
hippocampus,
upregulated
expression
calcium
signalling
regulation
genes,
whereas
depression-associated
deep
medial
prefrontal
cortex,
neuroplasticity
psychiatric
drug
target
genes.
Our
study
provides
demonstrates
gain
biological
insights
(such
trait-relevant
related
signature
genes)
these
maps.
Integration
enables
diseases
other
traits.
Development,
Journal Year:
2025,
Volume and Issue:
152(7)
Published: April 1, 2025
ABSTRACT
Pluripotency,
the
capacity
to
generate
all
cells
of
body,
is
a
defining
property
transient
population
epiblast
found
in
pre-,
peri-
and
post-implantation
mammalian
embryos.
As
development
progresses,
undergo
dynamic
transitions
pluripotency
states,
concurrent
with
specification
extra-embryonic
embryonic
lineages.
Recently,
stem
cell-based
models
pre-
human
have
been
developed
using
that
capture
key
properties
at
different
developmental
stages.
Here,
we
review
early
primate
development,
comparing
states
vivo
cultured
pluripotent
representative
these
states.
We
consider
how
status
starting
influences
embryo
and,
turn,
what
can
learn
about
epiblast.
Finally,
discuss
limitations
questions
arising
from
pioneering
studies
this
emerging
field.
Cell,
Journal Year:
2024,
Volume and Issue:
187(13), P. 3194 - 3219
Published: June 1, 2024
Developing
functional
organs
from
stem
cells
remains
a
challenging
goal
in
regenerative
medicine.
Existing
methodologies,
such
as
tissue
engineering,
bioprinting,
and
organoids,
only
offer
partial
solutions.
This
perspective
focuses
on
two
promising
approaches
emerging
for
engineering
human
cells:
cell-based
embryo
models
interspecies
organogenesis.
Both
exploit
the
premise
of
guiding
to
mimic
natural
development.
We
begin
by
summarizing
what
is
known
about
early
development
blueprint
recapitulating
organogenesis
both
chimeras.
The
latest
advances
fields
are
discussed
before
highlighting
technological
knowledge
gaps
be
addressed
developing
could
achieved
using
approaches.
conclude
discussing
challenges
facing
modeling
outlining
future
prospects
advancing
toward
generation
tissues
basic
research
translational
applications.
