Multiplexed
error-robust
fluorescence
in-situ
hybridization
(MERFISH)
allows
genome-scale
imaging
of
RNAs
in
individual
cells
intact
tissues.
To
date,
MERFISH
has
been
applied
to
image
thin
tissue
samples
∼10-µm
thickness.
Here,
we
present
a
thick-tissue
three-dimensional
(3D)
method,
which
uses
confocal
microscopy
for
optical
sectioning,
deep
learning
increasing
speed
and
quality,
as
well
sample
preparation
protocol
optimized
registration
thick
samples.
We
demonstrated
3D
on
mouse
brain
sections
up
200
µm
thickness
with
high
detection
efficiency
accuracy.
anticipate
that
will
broaden
the
scope
questions
can
be
addressed
by
spatial
genomics.
Limited
color
channels
in
fluorescence
microscopy
have
long
constrained
spatial
analysis
biological
specimens.
Here,
we
introduce
cycle
Hybridization
Chain
Reaction
(HCR),
a
method
that
integrates
multicycle
DNA
barcoding
with
HCR
to
overcome
this
limitation.
cycleHCR
enables
highly
multiplexed
imaging
of
RNA
and
proteins
using
unified
barcode
system.
Whole-embryo
transcriptomics
achieved
precise
three-dimensional
gene
expression
cell
fate
mapping
across
specimen
depth
~310
μm.
When
combined
expansion
microscopy,
revealed
an
intricate
network
10
subcellular
structures
mouse
embryonic
fibroblasts.
In
hippocampal
slices,
multiplex
protein
uncovered
complex
gradients
cell-type-specific
nuclear
structural
variations.
provides
quantitative
framework
for
elucidating
regulation
deep
tissue
contexts
research
potentially
diagnostic
applications.
International Journal of Genomics,
Год журнала:
2025,
Номер
2025(1)
Опубликована: Янв. 1, 2025
Rotator
cuff
injuries
are
a
common
cause
of
shoulder
pain
and
dysfunction,
with
chronic
inflammation
complicating
recovery.
Recent
advances
in
single‐cell
RNA
sequencing
(scRNA‐seq)
have
provided
new
insights
into
the
immune
cell
interactions
within
rotator
microenvironment
during
injury
healing.
This
review
focuses
on
application
scRNA‐seq
to
explore
roles
nonimmune
cells,
including
macrophages,
T‐cells,
fibroblasts,
myofibroblasts,
driving
inflammation,
tissue
repair,
fibrosis.
We
discuss
how
crosstalk
extracellular
matrix
influence
progression
healing
or
pathology.
Single‐cell
analyses
identified
distinct
molecular
signatures
associated
which
may
contribute
persistent
damage.
Additionally,
we
highlight
therapeutic
potential
targeting
emphasizing
personalized
medicine
approaches.
Overall,
integration
studying
enhances
our
understanding
cellular
mechanisms
involved
offers
perspectives
for
developing
targeted
treatments
regenerative
medicine.
Multiplexed
error-robust
fluorescence
in
situ
hybridization
(MERFISH)
allows
genome-scale
imaging
of
RNAs
individual
cells
intact
tissues.
To
date,
MERFISH
has
been
applied
to
image
thin-tissue
samples
~10
µm
thickness.
Here,
we
present
a
thick-tissue
three-dimensional
(3D)
method,
which
uses
confocal
microscopy
for
optical
sectioning,
deep
learning
increasing
speed
and
quality,
as
well
sample
preparation
protocol
optimized
thick
samples.
We
demonstrated
3D
on
mouse
brain
tissue
sections
up
200
thickness
with
high
detection
efficiency
accuracy.
anticipate
that
will
broaden
the
scope
questions
can
be
addressed
by
spatial
genomics.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Июль 25, 2023
Abstract
Multiplexed
error-robust
fluorescence
in-situ
hybridization
(MERFISH)
allows
genome-scale
imaging
of
RNAs
in
individual
cells
intact
tissues.
To
date,
MERFISH
has
been
applied
to
image
thin
tissue
samples
∼10-µm
thickness.
Here,
we
present
a
thick-tissue
three-dimensional
(3D)
method,
which
uses
confocal
microscopy
for
optical
sectioning,
deep
learning
increasing
speed
and
quality,
as
well
sample
preparation
protocol
optimized
registration
thick
samples.
We
demonstrated
3D
on
mouse
brain
sections
up
200
µm
thickness
with
high
detection
efficiency
accuracy.
anticipate
that
will
broaden
the
scope
questions
can
be
addressed
by
spatial
genomics.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 24, 2024
Abstract
Organ
development
is
guided
by
a
space-time
landscape
that
constraints
cell
behavior.
This
challenging
to
characterize
for
the
hair
follicle
–
most
abundant
mini
organ
due
its
complex
microscopic
structure
and
asynchronous
development.
We
developed
3DEEP,
tissue
clearing
spatial
transcriptomic
strategy
characterizing
blocks
up
400
µm
in
thickness.
captured
371
follicles
at
different
stages
of
organogenesis
1
mm
3
skin
12-hour-old
mouse
with
6
million
transcripts
from
81
genes.
From
this
single
time
point,
we
deconvoluted
age
based
on
whole-organ
molecular
pseudotimes
animate
stop-motion
3D
atlas
along
trajectory.
defined
characterized
order
emergence
structures,
differential
signaling
dynamics
top
bottom,
morphogen
shifts
preceding
accompanying
structural
changes,
series
changes
leading
formation
canal
opening.
further
found
stem
cells
their
niche
are
established
stratified
early
organogenesis,
before
bulb.
Overall,
work
demonstrates
power
increased
depth
transcriptomics
provide
four-dimensional
analysis
organogenesis.
Multiplexed
error-robust
fluorescence
in
situ
hybridization
(MERFISH)
allows
genome-scale
imaging
of
RNAs
individual
cells
intact
tissues.
To
date,
MERFISH
has
been
applied
to
image
thin-tissue
samples
~10
µm
thickness.
Here,
we
present
a
thick-tissue
three-dimensional
(3D)
method,
which
uses
confocal
microscopy
for
optical
sectioning,
deep
learning
increasing
speed
and
quality,
as
well
sample
preparation
protocol
optimized
thick
samples.
We
demonstrated
3D
on
mouse
brain
tissue
sections
up
200
thickness
with
high
detection
efficiency
accuracy.
anticipate
that
will
broaden
the
scope
questions
can
be
addressed
by
spatial
genomics.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 9, 2024
ABSTRACT
Spatial
omics
technologies
have
revolutionized
our
studies
on
tissue
architecture
and
cellular
interactions
at
single-cell
resolution.
While
spatial
multi-omics
approaches
offer
unprecedented
insights
into
complex
biological
systems,
their
widespread
adoption
is
hindered
by
technical
challenges,
specialized
requirements,
limited
accessibility.
To
address
these
limitations,
we
present
NicheTrans,
the
first
spatially-aware
cross-omics
translation
method
a
flexible
Transformer-based
multi-modal
deep
learning
framework.
Unlike
existing
(non-spatial)
methods,
NicheTrans
uniquely
incorporates
both
microenvironment
information
integration
of
data,
such
as
morphology
prior
knowledge.
We
validated
across
diverse
cases:
Parkinson’s
Disease
(PD),
Alzheimer’s
(AD),
breast
cancer,
lymph
nodes.
Our
approach
demonstrated
superior
performance
compared
to
highlighting
crucial
role
in
translation.
Through
uncovered
domains
that
were
not
detectable
through
single-omics
analysis
alone.
Model
interpretation
revealed
key
molecular
relationships,
including
gene
programs
associated
with
dopamine
metabolism
amyloid
β-associated
cell
states.
Additionally,
using
translated
protein
markers
landmarks,
quantified
organization
glial
subtypes
AD
brain.
represents
powerful
tool
for
generating
comprehensive
from
more
accessible
measurements,
making
feasible
broader
research
community.
