Proceedings of the National Academy of Sciences,
Год журнала:
2025,
Номер
122(10)
Опубликована: Март 5, 2025
Axolotls
are
amphibian
models
for
studying
nervous
system
evolution,
development,
and
regeneration.
Tools
to
visualize
manipulate
cells
of
the
axolotl
with
high-efficiency,
spatial
temporal
precision
therefore
greatly
required.
Recombinant
adeno-associated
viruses
(AAVs)
frequently
used
in
vivo
gene
transfer
but
virus-mediated
delivery
has
not
yet
been
described.
Here,
we
demonstrate
use
AAVs
efficient
within
brain,
spinal
cord,
retina.
We
show
that
serotypes
AAV8,
AAV9,
AAVPHP.eB
suitable
viral
vectors
infect
both
excitatory
inhibitory
neuronal
populations
brain.
further
AAV9
trace
retrograde
anterograde
projections
between
retina
brain
identify
a
cell
population
projecting
from
Together,
our
work
establishes
as
powerful
tool
interrogate
organization
axolotl.
Salamanders
are
tetrapod
models
to
study
brain
organization
and
regeneration;
however,
the
identity
evolutionary
conservation
of
cell
types
largely
unknown.
We
delineated
populations
in
axolotl
telencephalon
during
homeostasis
regeneration
using
single-cell
genomic
profiling.
identified
glutamatergic
neurons
with
similarities
amniote
hippocampus,
dorsal
lateral
cortex,
conserved
γ-aminobutyric
acid-releasing
(GABAergic)
neuron
classes.
inferred
transcriptional
dynamics
gene
regulatory
relationships
postembryonic,
region-specific
neurogenesis
unraveled
differentiation
signatures.
After
injury,
ependymoglia
activate
an
injury-specific
state
before
reestablishing
lost
axonal
connections.
Together,
our
analyses
yield
insights
into
organization,
evolution,
a
nervous
system.
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Окт. 14, 2023
The
growing
number
of
available
single-cell
gene
expression
datasets
from
different
species
creates
opportunities
to
explore
evolutionary
relationships
between
cell
types
across
species.
Cross-species
integration
RNA-sequencing
data
has
been
particularly
informative
in
this
context.
However,
order
do
so
robustly
it
is
essential
have
rigorous
benchmarking
and
appropriate
guidelines
ensure
that
results
truly
reflect
biology.
Here,
we
benchmark
28
combinations
homology
mapping
methods
algorithms
a
variety
biological
settings.
We
examine
the
capability
each
strategy
perform
species-mixing
known
homologous
preserve
heterogeneity
using
9
established
metrics.
also
develop
new
biology
conservation
metric
address
maintenance
type
distinguishability.
Overall,
scANVI,
scVI
SeuratV4
achieve
balance
conservation.
For
evolutionarily
distant
species,
including
in-paralogs
beneficial.
SAMap
outperforms
when
integrating
whole-body
atlases
with
challenging
annotation.
provide
our
freely
cross-species
assessment
pipeline
help
analyse
algorithms.
The
amniote
pallium
contains
sensory
circuits
that
are
structurally
and
functionally
equivalent,
yet
their
evolutionary
relationship
remains
unresolved.
We
used
birthdating
analysis,
single-cell
RNA
spatial
transcriptomics,
mathematical
modeling
to
compare
the
development
evolution
of
known
pallial
across
birds
(chick),
lizards
(gecko),
mammals
(mouse).
reveal
neurons
within
these
circuits’
stations
generated
at
varying
developmental
times
brain
regions
species
found
an
early
divergence
in
transcriptomic
progression
glutamatergic
neurons.
Our
research
highlights
distinctions
functional
similarities
circuit
between
mammals,
suggesting
convergence
high-order
processing
lineages.
Combinations
of
transcription
factors
govern
the
identity
cell
types,
which
is
reflected
by
genomic
enhancer
codes.
We
used
deep
learning
to
characterize
these
codes
and
devised
three
metrics
compare
types
in
telencephalon
across
amniotes.
To
this
end,
we
generated
single-cell
multiome
spatially
resolved
transcriptomics
data
chicken
telencephalon.
Enhancer
orthologous
nonneuronal
γ-aminobutyric
acid–mediated
(GABAergic)
show
a
high
degree
similarity
amniotes,
whereas
excitatory
neurons
mammalian
neocortex
avian
pallium
exhibit
varying
degrees
similarity.
mesopallial
are
most
similar
those
deep-layer
neurons.
With
study,
present
generally
applicable
approaches
on
basis
regulatory
sequences.
Innovations
in
the
pallium
likely
facilitated
evolution
of
advanced
cognitive
abilities
birds.
We
therefore
scrutinized
its
cellular
composition
and
using
cell
type
atlases
from
chicken,
mouse,
nonavian
reptiles.
found
that
avian
shares
most
inhibitory
neuron
types
with
other
amniotes.
Whereas
excitatory
amniote
hippocampal
regions
show
evolutionary
conservation,
those
pallial
have
diverged.
Neurons
mesopallium
display
gene
expression
profiles
akin
to
mammalian
claustrum
deep
cortical
layers,
while
certain
nidopallial
resemble
neurons
piriform
cortex.
Lastly,
we
observed
substantial
convergence
between
dorsally
located
hyperpallium
ventrally
nidopallium
during
late
development,
suggesting
topological
location
does
not
always
dictate
programs
determining
functional
properties
adult
pallium.
The
mammalian
brain
is
composed
of
many
structures,
each
with
its
own
ontogenetic
and
developmental
history.
We
used
single-nucleus
RNA
sequencing
to
sample
over
2.4
million
cells
across
18
locations
in
the
common
marmoset,
a
New
World
monkey
primed
for
genetic
engineering,
examined
gene
expression
patterns
cell
types
within
structures.
adult
transcriptomic
identity
most
neuronal
shaped
more
by
origin
than
neurotransmitter
signaling
repertoire.
Quantitative
mapping
GABAergic
single-molecule
FISH
(smFISH)
reveals
that
interneurons
striatum
neocortex
follow
distinct
spatial
principles,
lateral
prefrontal
other
higher-order
cortical
association
areas
are
distinguished
high
proportions
Nature Ecology & Evolution,
Год журнала:
2023,
Номер
7(10), С. 1714 - 1728
Опубликована: Сен. 14, 2023
Abstract
The
vertebrate
brain
emerged
more
than
~500
million
years
ago
in
common
evolutionary
ancestors.
To
systematically
trace
its
cellular
and
molecular
origins,
we
established
a
spatially
resolved
cell
type
atlas
of
the
entire
sea
lamprey—a
jawless
species
whose
phylogenetic
position
affords
reconstruction
ancestral
traits—based
on
extensive
single-cell
RNA-seq
situ
sequencing
data.
Comparisons
this
to
neural
data
from
mouse
other
jawed
vertebrates
unveiled
various
shared
features
that
enabled
types,
tissue
structures
gene
expression
programs
brain.
However,
our
analyses
also
revealed
key
tissues
types
arose
later
evolution.
For
example,
was
probably
devoid
cerebellar
oligodendrocytes
(myelinating
cells);
suggest
latter
astrocyte-like
precursors
lineage.
Altogether,
work
illuminates
architecture
provides
foundation
for
exploring
diversification
during
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Апрель 17, 2024
Abstract
Macroglia
fulfill
essential
functions
in
the
adult
vertebrate
brain,
producing
and
maintaining
neurons
regulating
neuronal
communication.
However,
we
still
know
little
about
their
emergence
diversification.
We
used
zebrafish
D.
rerio
as
a
distant
model
with
moderate
glial
diversity
anchor
to
reanalyze
datasets
covering
over
600
million
years
of
evolution.
identify
core
features
neurogenesis
innovations
mammalian
lineage
potential
link
rarity
radial
glia-like
cells
humans.
Our
results
also
suggest
that
associated
astrocytes
originated
multifunctional
cell
type
fulfilling
both
neural
stem
astrocytic
before
these
diverged.
Finally,
conserved
elements
macroglial
identity
function
time
during
