Science,
Journal Year:
2022,
Volume and Issue:
376(6594)
Published: May 12, 2022
Despite
their
crucial
role
in
health
and
disease,
our
knowledge
of
immune
cells
within
human
tissues
remains
limited.
We
surveyed
the
compartment
16
from
12
adult
donors
by
single-cell
RNA
sequencing
VDJ
generating
a
dataset
~360,000
cells.
To
systematically
resolve
cell
heterogeneity
across
tissues,
we
developed
CellTypist,
machine
learning
tool
for
rapid
precise
type
annotation.
Using
this
approach,
combined
with
detailed
curation,
determined
tissue
distribution
finely
phenotyped
types,
revealing
hitherto
unappreciated
tissue-specific
features
clonal
architecture
T
B
Our
multitissue
approach
lays
foundation
identifying
highly
resolved
types
leveraging
common
reference
dataset,
tissue-integrated
expression
analysis,
antigen
receptor
sequencing.
Nature Genetics,
Journal Year:
2021,
Volume and Issue:
53(3), P. 403 - 411
Published: Feb. 25, 2021
Abstract
The
advent
of
single-cell
chromatin
accessibility
profiling
has
accelerated
the
ability
to
map
gene
regulatory
landscapes
but
outpaced
development
scalable
software
rapidly
extract
biological
meaning
from
these
data.
Here
we
present
a
suite
for
analysis
in
R
(ArchR;
https://www.archrproject.com/
)
that
enables
fast
and
comprehensive
ArchR
provides
an
intuitive,
user-focused
interface
complex
analyses,
including
doublet
removal,
clustering
cell
type
identification,
unified
peak
set
generation,
cellular
trajectory
DNA
element-to-gene
linkage,
transcription
factor
footprinting,
mRNA
expression
level
prediction
multi-omic
integration
with
RNA
sequencing
(scRNA-seq).
Enabling
over
1.2
million
single
cells
within
8
h
on
standard
Unix
laptop,
is
end-to-end
will
accelerate
understanding
regulation
at
resolution
individual
cells.
Cell,
Journal Year:
2021,
Volume and Issue:
184(3), P. 792 - 809.e23
Published: Feb. 1, 2021
Tumor-infiltrating
myeloid
cells
(TIMs)
are
key
regulators
in
tumor
progression,
but
the
similarity
and
distinction
of
their
fundamental
properties
across
different
tumors
remain
elusive.
Here,
by
performing
a
pan-cancer
analysis
single
from
210
patients
15
human
cancer
types,
we
identified
distinct
features
TIMs
types.
Mast
nasopharyngeal
were
found
to
be
associated
with
better
prognosis
exhibited
an
anti-tumor
phenotype
high
ratio
TNF+/VEGFA+
cells.
Systematic
comparison
between
cDC1-
cDC2-derived
LAMP3+
cDCs
revealed
differences
transcription
factors
external
stimulus.
Additionally,
pro-angiogenic
tumor-associated
macrophages
(TAMs)
characterized
diverse
markers
composition
appeared
certain
somatic
mutations
gene
expressions.
Our
results
provide
systematic
view
highly
heterogeneous
suggest
future
avenues
for
rational,
targeted
immunotherapies.
Science,
Journal Year:
2020,
Volume and Issue:
367(6476), P. 405 - 411
Published: Jan. 24, 2020
More
diversity
at
the
top
A
detailed
knowledge
of
cell
differentiation
hierarchies
is
important
for
understanding
diverse
biological
processes
such
as
organ
development,
tissue
regeneration,
and
cancer.
Single-cell
RNA
sequencing
can
help
elucidate
these
hierarchies,
but
it
requires
reliable
computational
methods
predicting
lineage
trajectories.
Gulati
et
al.
developed
CytoTRACE,
a
framework
based
on
simple
observation
that
transcriptional
diversity—the
number
genes
expressed
in
cell—decreases
during
differentiation.
CytoTRACE
outperformed
other
several
test
cases
was
successfully
applied
to
study
cellular
healthy
tumor
tissue.
Science
,
this
issue
p.
405
Cell,
Journal Year:
2022,
Volume and Issue:
185(5), P. 881 - 895.e20
Published: Jan. 25, 2022
Post-acute
sequelae
of
COVID-19
(PASC)
represent
an
emerging
global
crisis.
However,
quantifiable
risk
factors
for
PASC
and
their
biological
associations
are
poorly
resolved.
We
executed
a
deep
multi-omic,
longitudinal
investigation
309
patients
from
initial
diagnosis
to
convalescence
(2-3
months
later),
integrated
with
clinical
data
patient-reported
symptoms.
resolved
four
PASC-anticipating
at
the
time
diagnosis:
type
2
diabetes,
SARS-CoV-2
RNAemia,
Epstein-Barr
virus
viremia,
specific
auto-antibodies.
In
gastrointestinal
PASC,
SARS-CoV-2-specific
CMV-specific
CD8+
T
cells
exhibited
unique
dynamics
during
recovery
COVID-19.
Analysis
symptom-associated
immunological
signatures
revealed
coordinated
immunity
polarization
into
endotypes,
exhibiting
divergent
acute
severity
PASC.
find
that
between
diminish
over
time,
leading
distinct
convalescent
immune
states.
Detectability
most
emphasizes
importance
early
disease
measurements
understanding
emergent
chronic
conditions
suggests
treatment
strategies.
Science,
Journal Year:
2021,
Volume and Issue:
374(6574)
Published: Dec. 16, 2021
T
cells
play
a
central
role
in
cancer
immunotherapy,
but
we
lack
systematic
comparison
of
the
heterogeneity
and
dynamics
tumor-infiltrating
across
types.
We
built
single-cell
RNA-sequencing
pan-cancer
atlas
for
316
donors
21
types
revealed
distinct
cell
composition
patterns.
found
multiple
state-transition
paths
exhaustion
CD8+
preference
those
among
different
tumor
Certain
populations
showed
specific
correlation
with
patient
properties
such
as
mutation
burden,
shedding
light
on
possible
determinants
microenvironment.
compositions
within
tumors
alone
could
classify
patients
into
groups
clinical
trait
specificity,
providing
new
insights
immunity
precision
immunotherapy
targeting
cells.
