Cancer Discovery,
Journal Year:
2021,
Volume and Issue:
12(1), P. 134 - 153
Published: Aug. 20, 2021
Abstract
Liver
metastasis,
the
leading
cause
of
colorectal
cancer
mortality,
exhibits
a
highly
heterogeneous
and
suppressive
immune
microenvironment.
Here,
we
sequenced
97
matched
samples
by
using
single-cell
RNA
sequencing
spatial
transcriptomics.
Strikingly,
metastatic
microenvironment
underwent
remarkable
reprogramming
immunosuppressive
cells
such
as
MRC1+
CCL18+
M2-like
macrophages.
We
further
developed
scMetabolism,
computational
pipeline
for
quantifying
metabolism,
observed
that
those
macrophages
harbored
enhanced
metabolic
activity.
Interestingly,
neoadjuvant
chemotherapy
could
block
this
status
restore
antitumor
balance
in
responsive
patients,
whereas
nonresponsive
patients
deteriorated
into
more
one.
Our
work
described
evolution
metastasis
uncovered
black
box
how
tumors
respond
to
chemotherapy.
Significance:
present
atlas
liver
found
metabolically
activated
sites.
Efficient
can
slow
down
activation,
raising
possibility
target
metabolism
pathways
metastasis.
This
article
is
highlighted
In
Issue
feature,
p.
1
Cell,
Journal Year:
2021,
Volume and Issue:
184(13), P. 3573 - 3587.e29
Published: May 31, 2021
The
simultaneous
measurement
of
multiple
modalities
represents
an
exciting
frontier
for
single-cell
genomics
and
necessitates
computational
methods
that
can
define
cellular
states
based
on
multimodal
data.
Here,
we
introduce
"weighted-nearest
neighbor"
analysis,
unsupervised
framework
to
learn
the
relative
utility
each
data
type
in
cell,
enabling
integrative
analysis
modalities.
We
apply
our
procedure
a
CITE-seq
dataset
211,000
human
peripheral
blood
mononuclear
cells
(PBMCs)
with
panels
extending
228
antibodies
construct
reference
atlas
circulating
immune
system.
Multimodal
substantially
improves
ability
resolve
cell
states,
allowing
us
identify
validate
previously
unreported
lymphoid
subpopulations.
Moreover,
demonstrate
how
leverage
this
rapidly
map
new
datasets
interpret
responses
vaccination
coronavirus
disease
2019
(COVID-19).
Our
approach
broadly
applicable
strategy
analyze
look
beyond
transcriptome
toward
unified
definition
identity.
Genome biology,
Journal Year:
2020,
Volume and Issue:
21(1)
Published: Feb. 7, 2020
Abstract
The
recent
boom
in
microfluidics
and
combinatorial
indexing
strategies,
combined
with
low
sequencing
costs,
has
empowered
single-cell
technology.
Thousands—or
even
millions—of
cells
analyzed
a
single
experiment
amount
to
data
revolution
biology
pose
unique
science
problems.
Here,
we
outline
eleven
challenges
that
will
be
central
bringing
this
emerging
field
of
forward.
For
each
challenge,
highlight
motivating
research
questions,
review
prior
work,
formulate
open
This
compendium
is
for
established
researchers,
newcomers,
students
alike,
highlighting
interesting
rewarding
problems
the
coming
years.
