Signal Transduction and Targeted Therapy,
Journal Year:
2022,
Volume and Issue:
7(1)
Published: Jan. 14, 2022
Abstract
Lung
adenocarcinoma
(LUAD)
and
squamous
carcinoma
(LUSC)
are
two
major
subtypes
of
non-small
cell
lung
cancer
with
distinct
pathologic
features
treatment
paradigms.
The
heterogeneity
can
be
attributed
to
genetic,
transcriptional,
epigenetic
parameters.
Here,
we
established
a
multi-omics
atlas,
integrating
52
single-cell
RNA
sequencing
2342
public
bulk
sequencing.
We
investigated
their
differences
in
genetic
amplification,
cellular
compositions,
expression
modules.
revealed
that
LUAD
LUSC
contained
amplifications
occurring
selectively
subclusters
AT2
basal
cells,
had
composition
modules
associated
poor
survival
cancer.
Malignant
stage-specific
gene
analyses
further
uncovered
critical
transcription
factors
genes
tumor
progression.
Moreover,
identified
proliferating
differentiating
properties
cells.
Overexpression
assays
ten
genes,
including
sub-cluster
markers
AQP5
KPNA2
,
indicated
functional
roles,
providing
potential
targets
for
early
diagnosis
Nature Communications,
Journal Year:
2021,
Volume and Issue:
12(1)
Published: Sept. 28, 2021
Differential
expression
analysis
in
single-cell
transcriptomics
enables
the
dissection
of
cell-type-specific
responses
to
perturbations
such
as
disease,
trauma,
or
experimental
manipulations.
While
many
statistical
methods
are
available
identify
differentially
expressed
genes,
principles
that
distinguish
these
and
their
performance
remain
unclear.
Here,
we
show
relative
is
contingent
on
ability
account
for
variation
between
biological
replicates.
Methods
ignore
this
inevitable
biased
prone
false
discoveries.
Indeed,
most
widely
used
can
discover
hundreds
genes
absence
differences.
To
exemplify
principles,
exposed
true
discoveries
injured
mouse
spinal
cord.
Nature Communications,
Journal Year:
2022,
Volume and Issue:
13(1)
Published: March 10, 2022
Abstract
Identification
of
cell
populations
often
relies
on
manual
annotation
clusters
using
established
marker
genes.
However,
the
selection
genes
is
a
time-consuming
process
that
may
lead
to
sub-optimal
annotations
as
markers
must
be
informative
both
individual
and
various
types
present
in
sample.
Here,
we
developed
computational
platform,
ScType,
which
enables
fully-automated
ultra-fast
cell-type
identification
based
solely
given
scRNA-seq
data,
along
with
comprehensive
database
background
information.
Using
six
datasets
from
human
mouse
tissues,
show
how
ScType
provides
unbiased
accurate
type
by
guaranteeing
specificity
positive
negative
across
types.
We
also
demonstrate
distinguishes
between
healthy
malignant
populations,
single-cell
calling
single-nucleotide
variants,
making
it
versatile
tool
for
anticancer
applications.
The
widely
applicable
method
deployed
an
interactive
web-tool
(
https://sctype.app
),
open-source
R-package.
Nature Communications,
Journal Year:
2021,
Volume and Issue:
12(1)
Published: Sept. 29, 2021
Abstract
Single-cell
RNA
sequencing
data
can
unveil
the
molecular
diversity
of
cell
types.
Cell
type
atlases
mouse
spinal
cord
have
been
published
in
recent
years
but
not
integrated
together.
Here,
we
generate
an
atlas
types
based
on
single-cell
transcriptomic
data,
unifying
available
datasets
into
a
common
reference
framework.
We
report
hierarchical
structure
postnatal
relationships,
with
location
providing
highest
level
organization,
then
neurotransmitter
status,
family,
and
finally,
dozens
refined
populations.
validate
combinatorial
marker
code
for
each
neuronal
map
their
spatial
distributions
adult
cord.
also
show
complex
lineage
relationships
among
Additionally,
develop
open-source
classifier,
SeqSeek,
to
facilitate
standardization
identification.
This
work
provides
view
types,
gene
expression
signatures,
organization.
Nature,
Journal Year:
2022,
Volume and Issue:
611(7936), P. 540 - 547
Published: Nov. 9, 2022
Abstract
A
spinal
cord
injury
interrupts
pathways
from
the
brain
and
brainstem
that
project
to
lumbar
cord,
leading
paralysis.
Here
we
show
spatiotemporal
epidural
electrical
stimulation
(EES)
of
1–3
applied
during
neurorehabilitation
4,5
(EES
REHAB
)
restored
walking
in
nine
individuals
with
chronic
injury.
This
recovery
involved
a
reduction
neuronal
activity
humans
walking.
We
hypothesized
this
unexpected
reflects
activity-dependent
selection
specific
subpopulations
become
essential
for
patient
walk
after
To
identify
these
putative
neurons,
modelled
technological
therapeutic
features
underlying
EES
mice.
single-nucleus
RNA
sequencing
6–9
spatial
transcriptomics
10,11
cords
mice
chart
spatially
resolved
molecular
atlas
then
employed
cell
type
12,13
prioritization
neurons
single
population
excitatory
interneurons
nested
within
intermediate
laminae
emerged.
Although
are
not
required
before
injury,
demonstrate
they
following
Augmenting
phenocopied
enabled
by
,
whereas
ablating
them
prevented
occurs
spontaneously
moderate
thus
identified
recovery-organizing
subpopulation
is
necessary
sufficient
regain
Moreover,
our
methodology
establishes
framework
using
cartography
produce
complex
behaviours.
Proceedings of the National Academy of Sciences,
Journal Year:
2021,
Volume and Issue:
118(22)
Published: May 17, 2021
Significance
Comparative
analysis
of
samples
from
two
biological
states,
such
as
stages
embryonic
development,
is
a
pressing
problem
in
single-cell
RNA
sequencing
(scRNA-seq).
A
key
challenge
to
detect
cell
subpopulations
whose
abundance
differs
between
the
states.
To
that
end,
we
develop
DA-seq,
multiscale
strategy
compare
cellular
distributions.
In
contrast
existing
unsupervised
clustering-based
analysis,
DA-seq
can
delineate
with
most
significant
discrepancy
states
and
potentially
reveal
important
changes
processes
are
undetectable
using
conventional
methods.
Science,
Journal Year:
2023,
Volume and Issue:
381(6664), P. 1338 - 1345
Published: Sept. 21, 2023
Axon
regeneration
can
be
induced
across
anatomically
complete
spinal
cord
injury
(SCI),
but
robust
functional
restoration
has
been
elusive.
Whether
restoring
neurological
functions
requires
directed
of
axons
from
specific
neuronal
subpopulations
to
their
natural
target
regions
remains
unclear.
To
address
this
question,
we
applied
projection-specific
and
comparative
single-nucleus
RNA
sequencing
identify
that
restore
walking
after
incomplete
SCI.
We
show
chemoattracting
guiding
the
transected
these
neurons
region
led
substantial
recovery
SCI
in
mice,
whereas
simply
lesion
had
no
effect.
Thus,
reestablishing
projections
characterized
forms
an
essential
part
axon
strategies
aimed
at
lost
functions.
