Nucleic Acids Research,
Journal Year:
2024,
Volume and Issue:
53(D1), P. D1173 - D1185
Published: Oct. 29, 2024
Abstract
Single-cell
lineage
tracing
(scLT)
is
a
powerful
technique
that
integrates
cellular
barcoding
with
single-cell
sequencing
technologies.
This
new
approach
enables
the
simultaneous
measurement
of
cell
fate
and
molecular
profiles
at
resolution,
uncovering
gene
regulatory
program
determination.
However,
comprehensive
scLT
database
not
yet
available.
Here,
we
present
(scLTdb,
https://scltdb.com)
containing
109
datasets
are
manually
curated
analyzed
through
standard
pipeline.
The
scLTdb
provides
interactive
analysis
modules
for
visualizing
re-analyzing
datasets,
especially
relationship
analysis.
Importantly,
also
allows
users
to
identify
fate-related
signatures.
In
conclusion,
an
interface
data
exploration
analysis,
will
facilitate
understanding
decision
commitment
in
development
diseases.
Nature,
Journal Year:
2024,
Volume and Issue:
627(8003), P. 389 - 398
Published: Jan. 22, 2024
Abstract
The
human
blood
system
is
maintained
through
the
differentiation
and
massive
amplification
of
a
limited
number
long-lived
haematopoietic
stem
cells
(HSCs)
1
.
Perturbations
to
this
process
underlie
diverse
diseases,
but
clonal
contributions
haematopoiesis
how
changes
with
age
remain
incompletely
understood.
Although
recent
insights
have
emerged
from
barcoding
studies
in
model
systems
2–5
,
simultaneous
detection
cell
states
phylogenies
natural
barcodes
humans
remains
challenging.
Here
we
introduce
an
improved,
single-cell
lineage-tracing
based
on
deep
naturally
occurring
mitochondrial
DNA
mutations
readout
transcriptional
chromatin
accessibility.
We
use
define
architecture
HSCs
map
physiological
state
output
clones.
uncover
functional
heterogeneity
HSC
clones,
which
stable
over
months
manifests
as
both
differences
total
biases
towards
production
different
mature
types.
also
find
that
diversity
clones
decreases
markedly
age,
leading
oligoclonal
structure
multiple
distinct
expansions.
Our
study
thus
provides
clonally
resolved
cell-state-aware
atlas
at
resolution,
showing
unappreciated
and,
more
broadly,
paving
way
for
refined
dynamics
across
range
tissues
health
disease.
ACS Nano,
Journal Year:
2024,
Volume and Issue:
18(17), P. 10979 - 11024
Published: April 18, 2024
Nanomaterials
have
attractive
physicochemical
properties.
A
variety
of
nanomaterials
such
as
inorganic,
lipid,
polymers,
and
protein
nanoparticles
been
widely
developed
for
nanomedicine
via
chemical
conjugation
or
physical
encapsulation
bioactive
molecules.
Superior
to
traditional
drugs,
nanomedicines
offer
high
biocompatibility,
good
water
solubility,
long
blood
circulation
times,
tumor-targeting
Capitalizing
on
this,
several
nanoformulations
already
clinically
approved
many
others
are
currently
being
studied
in
clinical
trials.
Despite
their
undoubtful
success,
the
molecular
mechanism
action
vast
majority
remains
poorly
understood.
To
tackle
this
limitation,
herein,
review
critically
discusses
strategy
applying
multiomics
analysis
study
nanomedicines,
named
nanomedomics,
including
advantages,
applications,
future
directions.
comprehensive
understanding
could
provide
valuable
insight
therefore
foster
development
translation
nanomedicines.
Journal of Translational Medicine,
Journal Year:
2025,
Volume and Issue:
23(1)
Published: March 4, 2025
Lineage
tracing
is
a
valuable
technique
that
has
greatly
facilitated
the
exploration
of
cell
origins
and
behavior.
With
continuous
development
single-cell
sequencing
technology,
lineage
technology
based
on
level
become
an
important
method
to
study
biological
development.
Single-cell
plays
role
in
hematological
system.
It
can
help
answer
many
questions,
such
as
heterogeneity
hematopoietic
stem
function
structure,
malignant
tumor
cells
Many
studies
have
been
conducted
explore
field
hematology
by
applying
this
technology.
This
review
focuses
superiority
emerging
technologies
Integration
barcodes,
CRISPR
barcoding,
base
editors,
summarizes
their
applications
These
suggested
vast
potential
unraveling
complex
cellular
behaviors
dynamics
both
normal
pathological
contexts.
Cell,
Journal Year:
2023,
Volume and Issue:
186(12), P. 2610 - 2627.e18
Published: May 19, 2023
The
hourglass
model
describes
the
convergence
of
species
within
same
phylum
to
a
similar
body
plan
during
development;
however,
molecular
mechanisms
underlying
this
phenomenon
in
mammals
remain
poorly
described.
Here,
we
compare
rabbit
and
mouse
time-resolved
differentiation
trajectories
revisit
at
single-cell
resolution.
We
modeled
gastrulation
dynamics
using
hundreds
embryos
sampled
between
gestation
days
6.0
8.5
compared
framework
for
differentiation-flows
analysis.
find
toward
cell-state
compositions
E7.5,
supported
by
quantitatively
conserved
expression
76
transcription
factors,
despite
divergence
surrounding
trophoblast
hypoblast
signaling.
However,
observed
noticeable
changes
specification
timing
some
lineages
primordial
germ
cell
programs,
which
do
not
activate
mesoderm
genes.
Comparative
analysis
temporal
models
provides
basis
studying
evolution
across
mammals.
Genome Medicine,
Journal Year:
2024,
Volume and Issue:
16(1)
Published: April 11, 2024
Abstract
Background
Most
primary
Triple
Negative
Breast
Cancers
(TNBCs)
show
amplification
of
the
Epidermal
Growth
Factor
Receptor
(EGFR)
gene,
leading
to
increased
protein
expression.
However,
unlike
other
EGFR-driven
cancers,
targeting
this
receptor
in
TNBC
yields
inconsistent
therapeutic
responses.
Methods
To
elucidate
underlying
mechanisms
variability,
we
employ
cellular
barcoding
and
single-cell
transcriptomics
reconstruct
subclonal
dynamics
EGFR-amplified
cells
response
afatinib,
a
tyrosine
kinase
inhibitor
(TKI)
that
irreversibly
inhibits
EGFR.
Results
Integrated
lineage
tracing
analysis
revealed
rare
pre-existing
subpopulation
with
distinct
biological
signature,
including
elevated
expression
levels
Insulin-Like
Binding
Protein
2
(IGFBP2).
We
IGFBP2
overexpression
is
sufficient
render
tolerant
afatinib
treatment
by
activating
compensatory
insulin-like
growth
factor
I
(IGF1-R)
signalling
pathway.
Finally,
based
on
reconstructed
resistance,
deep
learning
techniques
predict
sensitivity
cells.
Conclusions
Our
strategy
proved
effective
reconstructing
complex
network
driving
EGFR-targeted
therapy
offering
new
insights
for
development
individualized
strategies
TNBC.
