Journal of Proteome Research,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 28, 2025
Mass
spectrometry
imaging
(MSI)
has
revolutionized
the
study
of
tissue
metabolism
by
enabling
visualization
small
molecule
metabolites
(SMMs)
with
high
spatial
resolution.
However,
comprehensive
SMM
databases
for
different
organ
tissues
are
lacking,
hindering
our
understanding
metabolism.
To
address
this
resource
gap,
we
present
a
large-scale
gallery
mouse
brain,
kidney,
and
liver,
capturing
SMMs
spanning
eight
chemical
super
classes
encompassing
over
40
metabolic
pathways.
Manual
curation
display
these
data
sets
unveil
patterns
that
less
documented
in
reported
organs.
Specifically,
identify
65
brain
coronal
sections
71
sagittal
sections,
including
neurotransmitters.
Furthermore,
map
98
kidneys
66
providing
insights
into
their
amino
acid
glutathione
Our
insightful
serves
as
critical
research
community,
filling
significant
gap.
This
is
freely
available
download
can
be
accessed
through
BioImage
Archive
METASPACE
repositories,
high-quality
annotated
images
potential
future
computational
models
advancing
at
level.
Signal Transduction and Targeted Therapy,
Journal Year:
2023,
Volume and Issue:
8(1)
Published: March 20, 2023
Metabolic
abnormalities
lead
to
the
dysfunction
of
metabolic
pathways
and
metabolite
accumulation
or
deficiency
which
is
well-recognized
hallmarks
diseases.
Metabolite
signatures
that
have
close
proximity
subject's
phenotypic
informative
dimension,
are
useful
for
predicting
diagnosis
prognosis
diseases
as
well
monitoring
treatments.
The
lack
early
biomarkers
could
poor
serious
outcomes.
Therefore,
noninvasive
methods
with
high
specificity
selectivity
desperately
needed.
Small
molecule
metabolites-based
metabolomics
has
become
a
specialized
tool
biomarker
pathway
analysis,
revealing
possible
mechanisms
human
various
deciphering
therapeutic
potentials.
It
help
identify
functional
related
variation
delineate
biochemical
changes
indicators
pathological
damage
prior
disease
development.
Recently,
scientists
established
large
number
profiles
reveal
underlying
networks
target
exploration
in
biomedicine.
This
review
summarized
analysis
on
potential
value
small-molecule
candidate
metabolites
clinical
events,
may
better
diagnosis,
prognosis,
drug
screening
treatment.
We
also
discuss
challenges
need
be
addressed
fuel
next
wave
breakthroughs.
Nature Metabolism,
Journal Year:
2022,
Volume and Issue:
4(9), P. 1109 - 1118
Published: Aug. 25, 2022
Abstract
A
common
drawback
of
metabolic
analyses
complex
biological
samples
is
the
inability
to
consider
cell-to-cell
heterogeneity
in
context
an
organ
or
tissue.
To
overcome
this
limitation,
we
present
advanced
high-spatial-resolution
metabolomics
approach
using
matrix-assisted
laser
desorption/ionization
mass
spectrometry
imaging
(MALDI-MSI)
combined
with
isotope
tracing.
This
method
allows
mapping
cell-type-specific
dynamic
changes
central
carbon
metabolism
a
heterogeneous
tissue
architecture,
such
as
kidney.
Combined
multiplexed
immunofluorescence
staining,
can
detect
and
nutrient
partitioning
targeted
cell
types,
demonstrated
bilateral
renal
ischemia–reperfusion
injury
(bIRI)
experimental
model.
Our
enables
us
identify
region-specific
perturbations
associated
lesion
throughout
recovery,
including
unexpected
anomalies
cells
apparently
normal
phenotype
recovery
phase.
These
findings
may
be
relevant
understanding
homeostatic
capacity
kidney
microenvironment.
In
sum,
achieve
resolution
at
single-cell
level
situ
hence
interpret
dynamics
structure
neighboring
cells.
Cell stem cell,
Journal Year:
2022,
Volume and Issue:
29(11), P. 1580 - 1593.e7
Published: Nov. 1, 2022
Accumulating
evidence
demonstrates
important
roles
for
metabolism
in
cell
fate
determination.
However,
it
is
a
challenge
to
assess
at
spatial
resolution
that
acknowledges
both
heterogeneity
and
cellular
dynamics
its
tissue
microenvironment.
Using
multi-omics
platform
study
cell-type-specific
complex
tissues,
we
describe
the
metabolic
trajectories
during
nephrogenesis
developing
human
kidney.
Exploiting
situ
analysis
of
isotopic
labeling,
shift
from
glycolysis
toward
fatty
acid
β-oxidation
was
observed
differentiation
renal
vesicle
S-shaped
body
proximal
tubules.
In
addition,
show
hiPSC-derived
kidney
organoids
are
characterized
by
immature
phenotype
fails
use
mitochondrial
long-chain
acids
energy
metabolism.
Furthermore,
supplementation
butyrate
enhances
tubular
epithelial
maturation
cultured
organoids.
Our
findings
highlight
relevance
understanding
efficiently
guide
stem
differentiation.
Cell Metabolism,
Journal Year:
2024,
Volume and Issue:
36(5), P. 1105 - 1125.e10
Published: March 20, 2024
A
large-scale
multimodal
atlas
that
includes
major
kidney
regions
is
lacking.
Here,
we
employed
simultaneous
high-throughput
single-cell
ATAC/RNA
sequencing
(SHARE-seq)
and
spatially
resolved
metabolomics
to
profile
54
human
samples
from
distinct
anatomical
regions.
We
generated
transcriptomes
of
446,267
cells
chromatin
accessibility
profiles
401,875
developed
a
package
analyze
408,218
metabolomes.
find
the
same
cell
type,
including
thin
limb,
thick
ascending
limb
loop
Henle
principal
cells,
display
transcriptomic,
accessibility,
metabolomic
signatures,
depending
on
anatomic
location.
Surveying
metabolism-associated
gene
revealed
non-overlapping
metabolic
signatures
between
nephron
segments
dysregulated
lipid
metabolism
in
diseased
proximal
tubule
(PT)
cells.
Integrating
omics
with
clinical
data
identified
PLEKHA1
as
disease
marker,
its
vitro
knockdown
increased
expression
PT
differentiation,
suggesting
possible
pathogenic
roles.
This
study
highlights
previously
underrepresented
cellular
heterogeneity
underlying
anatomy.
Genome Medicine,
Journal Year:
2024,
Volume and Issue:
16(1)
Published: Jan. 18, 2024
Abstract
Spatial
multi-omic
studies
have
emerged
as
a
promising
approach
to
comprehensively
analyze
cells
in
tissues,
enabling
the
joint
analysis
of
multiple
data
modalities
like
transcriptome,
epigenome,
proteome,
and
metabolome
parallel
or
even
same
tissue
section.
This
review
focuses
on
recent
advancements
spatial
multi-omics
technologies,
including
novel
computational
approaches.
We
discuss
low-resolution
high-resolution
methods
which
can
resolve
up
10,000
individual
molecules
at
subcellular
level.
By
applying
integrating
these
techniques,
researchers
recently
gained
valuable
insights
into
molecular
circuits
mechanisms
govern
cell
biology
along
cardiovascular
disease
spectrum.
provide
an
overview
current
approaches,
with
focus
integration
datasets,
highlighting
strengths
weaknesses
various
pipelines.
These
tools
play
crucial
role
analyzing
interpreting
facilitating
discovery
new
findings,
enhancing
translational
research.
Despite
nontrivial
challenges,
such
need
for
standardization
experimental
setups,
analysis,
improved
tools,
application
holds
tremendous
potential
revolutionizing
our
understanding
human
processes
identification
biomarkers
therapeutic
targets.
Exciting
opportunities
lie
ahead
field
will
likely
contribute
advancement
personalized
medicine
diseases.
