bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2022,
Volume and Issue:
unknown
Published: Dec. 2, 2022
Abstract
Tissue
clearing
and
labeling
techniques
have
revolutionized
brain-wide
imaging
analysis,
yet
their
application
to
clinical
formalin-fixed
paraffin-embedded
(FFPE)
blocks
remains
challenging.
We
introduce
HIF-Clear,
a
novel
method
for
efficiently
centimeter-thick
FFPE
specimens
using
elevated
temperature
concentrated
detergents.
HIF-Clear
with
multi-round
immunolabeling
reveals
neuron
circuitry
regulating
multiple
neurotransmitter
systems
in
whole
mouse
brain,
is
able
be
used
as
the
evaluation
of
disease
treatment
efficiency.
also
supports
expansion
microscopy
can
performed
on
non-sectioned
15-year-old
specimen,
well
3-month
brain.
Thus,
represents
feasible
approach
researching
archived
future
neuroscientific
3D
neuropathological
analyses.
Frontiers in Neural Circuits,
Journal Year:
2024,
Volume and Issue:
18
Published: April 17, 2024
Novel
brain
clearing
methods
revolutionize
imaging
by
increasing
visualization
throughout
the
at
high
resolution.
However,
combining
standard
tool
of
immunostaining
targets
interest
with
has
lagged
behind.
We
integrate
whole-mount
PEGASOS
tissue
clearing,
referred
to
as
iPEGASOS
(immunostaining-compatible
PEGASOS),
address
challenge
signal
quenching
during
processes.
effectively
enhances
molecular-genetically
targeted
fluorescent
signals
that
are
otherwise
compromised
conventional
procedures.
Additionally,
we
demonstrate
utility
for
visualizing
neurochemical
markers
or
viral
labels
augment
transgenic
mouse
lines
cannot
provide.
Our
study
encompasses
three
distinct
applications,
each
showcasing
versatility
and
efficacy
this
approach.
employ
enhance
molecular
in
reporter
visualize
whole-brain
spatial
distribution
specific
cellular
populations.
also
significantly
improve
neural
circuit
connections
enhancing
from
tracers
injected
into
brain.
Last,
show
without
genetic
selectively
label
beta-amyloid
deposits
a
model
Alzheimer's
disease,
facilitating
comprehensive
pathological
features.
Science,
Journal Year:
2024,
Volume and Issue:
386(6724), P. 907 - 915
Published: Nov. 21, 2024
Recent
advances
in
RNA
analysis
have
deepened
our
understanding
of
cellular
states
biological
tissues.
However,
a
substantial
gap
remains
integrating
expression
data
with
spatial
context
across
organs,
primarily
owing
to
the
challenges
associated
detection
within
intact
tissue
volumes.
Here,
we
developed
Tris
buffer–mediated
retention
situ
hybridization
chain
reaction
signal
cleared
organs
(TRISCO),
an
effective
tissue-clearing
method
designed
for
whole-brain
three-dimensional
(3D)
imaging.
TRISCO
resolved
several
crucial
issues,
including
preservation
integrity,
achieving
uniform
labeling,
and
enhancing
transparency.
We
tested
using
broad
range
cell-identity
markers,
noncoding
activity-dependent
RNAs,
diverse
varying
sizes
species.
thus
emerges
as
powerful
tool
single-cell,
whole-brain,
3D
imaging
that
enables
comprehensive
transcriptional
entire
brain.
Chemical & Biomedical Imaging,
Journal Year:
2024,
Volume and Issue:
2(8), P. 542 - 559
Published: June 18, 2024
The
quest
for
high
spatial
resolution
in
molecular
identification
is
critical
across
various
domains,
including
physiology,
pathology,
and
pharmaceutical
research.
Super-resolution
microscopy
has
made
strides
by
surpassing
the
Abbe
diffraction
limit,
but
it
relies
on
sophisticated
equipment
limited
sample
size
to
handle.
Expansion
microscopy,
an
emerging
technique,
broadened
scope
of
subdiffraction
imaging.
It
chemically
preserves
tissues
at
a
large
scale
physically
enlarges
them
4–20
times
linearly,
enabling
super-resolution
observation.
This
review
begins
exploring
foundational
concepts
tissue
clearing
latest
methodologies
field.
then
delves
into
core
tenets
expansion
covering
range
protocols.
spotlights
advancements
enhancing
resolution,
improving
labeling
efficiency,
ensuring
isotropic
expansion.
Finally,
offers
insights
prospective
evolution
microscopy.
emphasizes
potential
role
machine
learning
refining
image
quality
autonomous
extraction
data,
which
could
revolutionize
way
we
visualize
understand
biological
tissues.
Cancer Science,
Journal Year:
2024,
Volume and Issue:
115(4), P. 1029 - 1038
Published: Feb. 5, 2024
Here,
we
summarize
the
literature
relevant
to
recent
advances
in
three-dimensional
(3D)
histopathology
relation
clinical
oncology,
highlighting
serial
sectioning,
tissue
clearing,
light-sheet
microscopy,
and
digital
image
analysis
with
artificial
intelligence.
We
look
forward
a
future
where
3D
expands
our
understanding
of
human
pathophysiology
improves
patient
care
through
cross-disciplinary
collaboration
innovation.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: May 30, 2024
Abstract
Biological
systems
are
complex,
encompassing
intertwined
spatial,
molecular
and
functional
features.
However,
methodological
constraints
always
limit
the
completeness
of
information
that
can
be
extracted.
Here,
we
report
development
INSIHGT,
a
minimally
perturbative,
accessible
cost-efficient
three-dimensional
(3D)
spatial
biology
method
utilizing
superchaotropes
host-guest
chemistry.
This
allows
highly
multiplexed
multi-modal
readout
tissue
biomolecules
in
biological
up
to
centimeter
scales,
permitting
radio-histological
correlation
phosphorylated
alpha-synuclein
pathologies
human
hemi-brainstem.
The
homogeneous
penetration
permits
reliable
semi-quantitative
signals
3D
compared
reference
signals.
Diverse
antigens,
mRNA
transcripts,
neurotransmitters,
post-translational
epigenetic
modifications,
well-preserved
visualized.
INSIHGT
also
multi-round
probing
for
high-dimensional
compatibility
with
downstream
traditional
histology.
With
mapped
previously
undescribed
podocyte-to-parietal
epithelial
cell
microfilaments
demonstrated
their
geodesic
clustering
mouse
glomeruli,
catalogued
sparsely
located
neurofilament-intensive
inclusion
bodies
cerebellum,
identified
NPY-proximal
types
defined
by
morpho-proteomics
hypothalamus.
We
anticipate
form
foundations
multi-omics
technology
holistic
studies.
Materials Today Bio,
Journal Year:
2024,
Volume and Issue:
26, P. 101109 - 101109
Published: June 1, 2024
The
intricate
interplay
between
biochemical
and
physical
cues
dictates
pluripotent
stem
cell
(PSC)
differentiation
to
form
various
tissues.
While
modulation
has
been
extensively
studied,
the
role
of
biophysical
microenvironments
in
early
lineage
commitment
remains
elusive.
Here,
we
introduce
a
novel
3D
culture
system
combining
electrospun
nanofibers
with
microfabricated
polydimethylsiloxane
(PDMS)
patterns.
This
enables
controlled
formation
semispherical
human
induced
(hiPSC)
colonies,
facilitating
investigation
local
mechanical
niches
on
mechano-responsive
signaling
specification.
Our
unveiled
spatially
organized
RhoA
activity
coupled
actin-myosin
cable
formation,
suggesting
mechano-dependent
hiPSC
behaviors.
Nodal
network
analysis
RNA-seq
data
revealed
downstream
regulation
YAP
signaling,
DNA
histone
modifications,
patterned
germ
layer
Notably,
altering
colony
morphology
through
PDMS
microwell
shaping
effectively
modulated
spatial
distribution
mechano-sensitive
mediators
subsequent
differentiation.
study
provides
platform
decipher
embryogenesis,
offering
valuable
insights
for
material
design
tissue
engineering
regenerative
medicine
applications.
Tissue-clearing
and
labeling
techniques
have
revolutionized
brain-wide
imaging
analysis,
yet
their
application
to
clinical
formalin-fixed
paraffin-embedded
(FFPE)
blocks
remains
challenging.
We
introduce
HIF-Clear,
a
novel
method
for
efficiently
clearing
centimeter-thick
FFPE
specimens
using
elevated
temperature
concentrated
detergents.
HIF-Clear
with
multi-round
immunolabeling
reveals
neuron
circuitry
regulating
multiple
neurotransmitter
systems
in
whole
mouse
brain
is
able
be
used
as
the
evaluation
of
disease
treatment
efficiency.
also
supports
expansion
microscopy
can
performed
on
non-sectioned
15-year-old
specimen,
well
3-month
brain.
Thus,
represents
feasible
approach
researching
archived
future
neuroscientific
3D
neuropathological
analyses.
