Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments
npj Precision Oncology,
Год журнала:
2025,
Номер
9(1)
Опубликована: Март 11, 2025
The
tumor
microenvironment
(TME)
plays
a
crucial
role
in
orchestrating
cell
behavior
and
cancer
progression.
Recent
advances
spatial
profiling
technologies
have
uncovered
novel
signatures,
including
univariate
distribution
patterns,
bivariate
relationships,
higher-order
structures.
These
signatures
the
potential
to
revolutionize
mechanism
treatment.
In
this
review,
we
summarize
current
state
of
signature
research,
highlighting
computational
methods
uncover
spatially
relevant
biological
significance.
We
discuss
impact
these
on
fundamental
biology
translational
address
challenges
future
research
directions.
Язык: Английский
Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Март 11, 2025
Recent
breakthroughs
in
spatial
transcriptomics
technologies
have
enhanced
our
understanding
of
diverse
cellular
identities,
compositions,
interactions,
organizations,
and
functions.
Yet
existing
tools
are
still
limited
either
transcriptomic
coverage
or
resolution.
Leading
spatial-capture
spatial-tagging
techniques
that
rely
on
in-vitro
sequencing
offer
whole-transcriptome
coverage,
principle,
but
at
the
cost
lower
resolution
compared
to
image-based
techniques.
In
contrast,
high-performance
techniques,
which
situ
hybridization
sequencing,
achieve
single-molecule
retain
sub-cellular
morphologies,
by
probe
libraries
target
only
a
subset
transcriptome,
typically
covering
several
hundred
few
thousand
transcript
species.
Together,
these
limitations
hinder
unbiased,
hypothesis-free
analyses
high
Here
we
develop
new
technology
termed
Reverse-padlock
Amplicon
Encoding
FISH
(RAEFISH)
with
whole-genome
level
while
retaining
intact
tissues.
We
demonstrate
targeting
23,000
human
species
22,000
mouse
species,
including
nearly
entire
protein-coding
transcriptome
long-noncoding
RNAs,
single
cells
cultures
tissue
sections.
Our
reveal
differential
subcellular
localizations
transcripts,
cell-type-specific
cell-type-invariant
zonation
dependent
gene
expression
programs
underlying
preferential
cell-cell
interactions.
Finally,
further
for
direct
readout
gRNAs
an
high-content
CRISPR
screen.
Overall,
developments
provide
research
community
broadly
applicable
enables
high-coverage,
high-resolution
profiling
both
long
short,
native
engineered
RNA
many
biomedical
contexts.
Язык: Английский
Unraveling the future of genomics: CRISPR, single-cell omics, and the applications in cancer and immunology
Frontiers in Genome Editing,
Год журнала:
2025,
Номер
7
Опубликована: Апрель 11, 2025
The
CRISPR
system
has
transformed
many
research
areas,
including
cancer
and
immunology,
by
providing
a
simple
yet
effective
genome
editing
system.
Its
simplicity
facilitated
large-scale
experiments
to
assess
gene
functionality
across
diverse
biological
contexts,
generating
extensive
datasets
that
boosted
the
development
of
computational
methods
machine
learning/artificial
intelligence
applications.
Integrating
with
single-cell
technologies
further
advanced
our
understanding
function
its
role
in
processes,
unprecedented
insights
into
human
biology
disease
mechanisms.
This
powerful
combination
accelerated
AI-driven
analyses,
enhancing
diagnostics,
risk
prediction,
therapeutic
innovations.
review
provides
comprehensive
overview
CRISPR-based
systems,
highlighting
their
advancements,
current
progress,
challenges,
future
opportunities,
especially
immunology.
Язык: Английский