NAR Genomics and Bioinformatics,
Journal Year:
2025,
Volume and Issue:
7(2)
Published: March 29, 2025
Abstract
Supervised
and
unsupervised
methods
have
emerged
to
address
the
complexity
of
single
cell
data
analysis
in
context
large
pools
independent
studies.
Here,
we
present
ClusterFoldSimilarity
(CFS),
a
novel
statistical
method
design
quantify
similarity
between
groups
across
any
number
datasets,
without
need
for
correction
or
integration.
By
bypassing
these
processes,
CFS
avoids
introduction
artifacts
loss
information,
offering
simple,
efficient,
scalable
solution.
This
match
cells
that
exhibit
conserved
phenotypes
including
different
tissues
species,
multimodal
scenario,
single-cell
RNA-Seq,
ATAC-Seq,
proteomics,
or,
more
broadly,
exhibiting
differential
abundance
effects
among
cells.
Additionally,
performs
feature
selection,
obtaining
cross-dataset
markers
similar
observed,
providing
an
inherent
interpretability
relationships
populations.
To
showcase
effectiveness
our
methodology,
generated
single-nuclei
RNA-Seq
from
motor
cortex
spinal
cord
adult
mice.
using
CFS,
identified
three
distinct
sub-populations
astrocytes
on
both
tissues.
includes
various
visualization
interpretation
scores
Cellular and Molecular Immunology,
Journal Year:
2023,
Volume and Issue:
20(5), P. 432 - 447
Published: March 22, 2023
Abstract
Dendritic
cells
(DCs)
exhibit
a
specialized
antigen-presenting
function
and
play
crucial
roles
in
both
innate
adaptive
immune
responses.
Due
to
their
ability
cross-present
tumor
cell-associated
antigens
naïve
T
cells,
DCs
are
instrumental
the
generation
of
specific
T-cell-mediated
antitumor
effector
responses
control
growth
cell
dissemination.
Within
an
immunosuppressive
microenvironment,
DC
functions
can,
however,
be
severely
impaired.
In
this
review,
we
focus
on
mechanisms
capture
activation
by
role
microenvironment
shaping
functions,
taking
advantage
recent
studies
showing
phenotype
acquisition,
transcriptional
state
functional
programs
revealed
scRNA-seq
analysis.
The
therapeutic
potential
DC-mediated
antigen
sensing
priming
immunity
is
also
discussed.
Science Immunology,
Journal Year:
2022,
Volume and Issue:
7(70)
Published: April 1, 2022
Dendritic
cells
(DCs)
are
professional
antigen-presenting
cells,
orchestrating
innate
and
adaptive
immunity
during
infections,
autoimmune
diseases,
malignancies.
Since
the
discovery
of
DCs
almost
50
years
ago,
our
understanding
their
biology
in
humans
has
increased
substantially.
Here,
we
review
both
antitumor
tolerogenic
DC
responses
cancer
discuss
lineage-specific
contributions
by
functionally
specialized
subsets,
including
conventional
(cDC)
subsets
cDC1
cDC2,
newly
described
DC3,
plasmacytoid
(pDCs),
focusing
on
human
setting.
In
addition,
lineage-unrestricted
"mature
enriched
immunoregulatory
molecules"
(mregDC)
state
recently
across
different
tumors.
Cancer Discovery,
Journal Year:
2023,
Volume and Issue:
13(12), P. 2610 - 2631
Published: Sept. 27, 2023
Abstract
Cancer
mortality
primarily
stems
from
metastatic
recurrence,
emphasizing
the
urgent
need
for
developing
effective
metastasis-targeted
immunotherapies.
To
better
understand
cellular
and
molecular
events
shaping
niches,
we
used
a
spontaneous
breast
cancer
lung
metastasis
model
to
create
single-cell
atlas
spanning
different
stages
regions.
We
found
that
premetastatic
lungs
are
infiltrated
by
inflammatory
neutrophils
monocytes,
followed
accumulation
of
suppressive
macrophages
with
emergence
metastases.
Spatial
profiling
revealed
metastasis-associated
immune
cells
were
present
in
core,
exception
TREM2+
regulatory
uniquely
enriched
at
invasive
margin,
consistent
across
both
murine
models
human
patient
samples.
These
(Mreg)
contribute
formation
an
immune-suppressive
niche,
cloaking
tumor
surveillance.
Our
study
provides
compendium
cell
dynamics
informing
development
metastasis-targeting
Significance:
Temporal
spatial
analysis
new
players
modulating
surveillance
suppression.
highlights
distinct
populations
TREM2
as
modulators
microenvironment
metastasis,
key
determinant
defining
pointing
myeloid
checkpoints
improve
therapeutic
strategies.
This
article
is
featured
Selected
Articles
Issue,
p.
2489
Microorganisms,
Journal Year:
2024,
Volume and Issue:
12(4), P. 775 - 775
Published: April 11, 2024
Immune
system
aging
is
becoming
a
field
of
increasing
public
health
interest
because
prolonged
life
expectancy,
which
not
paralleled
by
an
increase
in
expectancy.
As
age
progresses,
innate
and
adaptive
immune
systems
undergo
changes,
are
defined,
respectively,
as
inflammaging
senescence.
A
wealth
available
data
demonstrates
that
these
two
conditions
closely
linked,
leading
to
greater
vulnerability
elderly
subjects
viral,
bacterial,
opportunistic
infections
well
lower
post-vaccination
protection.
To
face
this
novel
scenario,
in-depth
assessment
the
players
involved
changing
epidemiology
demanded
regarding
individual
concerted
involvement
cells
mediators
within
endogenous
exogenous
factors
co-morbidities.
This
review
provides
overall
updated
description
changes
affecting
system,
may
be
help
understanding
underlying
mechanisms
associated
with
main
age-associated
infectious
diseases.
Cytometry Part A,
Journal Year:
2024,
Volume and Issue:
105(6), P. 430 - 436
Published: April 18, 2024
Abstract
We
report
the
development
of
an
optimized
50‐color
spectral
flow
cytometry
panel
designed
for
in‐depth
analysis
immune
system
in
human
blood
and
tissues,
with
goal
maximizing
amount
information
that
can
be
collected
using
currently
available
platforms.
established
tested
this
peripheral
mononuclear
cells
(PBMCs),
but
included
CD45
to
enable
its
future
use
tissue
samples.
The
contains
lineage
markers
all
major
cell
subsets,
extensive
set
phenotyping
focused
on
activation
differentiation
status
T
dendritic
(DC)
compartment.
outline
biological
insight
gained
from
simultaneous
measurement
such
a
large
number
proteins
propose
approach
provides
unique
opportunity
comprehensive
exploration
samples
limited
cells.
Of
note,
we
compatible
sorting
further
downstream
applications.
Furthermore,
facilitate
wide‐spread
implementation
across
different
cohorts
samples,
trimmed‐down
45‐color
version
which
used
Finally,
generate
panel,
utilized
not
only
existing
design
guidelines,
also
developed
new
metrics
systematically
identify
optimal
combination
50
fluorochromes
evaluate
fluorochrome‐specific
resolution
context
unmixing
matrix.
Blood,
Journal Year:
2023,
Volume and Issue:
142(16), P. 1339 - 1347
Published: Aug. 18, 2023
Abstract
In
this
spotlight,
we
review
technical
issues
that
compromise
single-cell
analysis
of
tissue
macrophages,
including
limited
and
unrepresentative
yields,
fragmentation
generation
remnants,
activation
during
disaggregation.
These
may
lead
to
a
misleading
definition
subpopulations
macrophages
the
expression
macrophage-specific
transcripts
by
unrelated
cells.
Recognition
limitations
approaches
is
required
in
order
map
full
spectrum
tissue-resident
macrophage
heterogeneity
assess
its
biological
significance.
