bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 17, 2024
Lipids
represent
the
most
diverse
pool
of
metabolites
found
in
cells,
facilitating
compartmentation,
signaling,
and
other
functions.
Dysregulation
lipid
metabolism
is
linked
to
disease
states
such
as
cancer
neurodegeneration.
However,
limited
tools
are
available
for
quantifying
metabolic
fluxes
across
lipidome.
To
directly
measure
reaction
encompassing
compound
homeostasis,
we
applied
stable
isotope
tracing,
liquid
chromatography-high-resolution
mass
spectrometry,
network-based
isotopologue
modeling
non-small
cell
lung
(NSCLC)
models.
Compound
flux
analysis
(CL-MFA)
enables
concurrent
quantitation
fatty
acid
synthesis,
elongation,
headgroup
assembly,
salvage
reactions
within
virtually
any
biological
system.
Here,
resolve
liver
kinase
B1
(LKB1)-mediated
regulation
sphingolipid
recycling
NSCLC
cells
precision-cut
slice
cultures.
We
also
demonstrate
that
widely
used
tissue
culture
conditions
drive
upregulate
synthase
supraphysiological
levels.
Finally,
identify
previously
uncharacterized
isozyme
specificity
ceramide
inhibitors.
These
results
highlight
ability
CL-MFA
quantify
cycling
systems
discover
function
elucidate
molecular
mechanisms
membrane
metabolism.
Trends in Cell Biology,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
Lipids
are
major
cell
constituents
endowed
with
astonishing
structural
diversity.
The
pathways
responsible
for
the
assembly
and
disposal
of
different
lipid
species
energetically
demanding,
genes
encoding
metabolic
factors
lipid-related
proteins
comprise
a
sizable
fraction
our
coding
genome.
Despite
importance
lipids,
biological
significance
diversity
remains
largely
obscure.
Recent
technological
developments
have
enabled
extensive
analysis
at
single
level,
revealing
unexpected
cell-cell
variability
in
composition.
This
new
evidence
suggests
that
is
exploited
multicellularity
lipids
role
establishment
maintenance
identity.
In
this
review,
we
highlight
emerging
concepts
technologies
implications
research
future
studies.
Precise
and
dynamic
observation
of
redox
reactions
in
living
organisms
holds
significant
importance
for
the
study
physiological
processes
pathological
mechanisms.
However,
current
technologies
still
make
it
challenging
to
monitor
this
process
a
nondestructive
highly
sensitive
manner.
Herein,
we
introduced
bioactive
laser
approach
ultrasensitive
real-time
monitoring
intracellular
reactions.
Resazurin,
as
popular
cell
viability
assay
reagent,
has
lasing
behaviors
photostability,
which
makes
suitable
development
lasers.
Due
strong
interactions
light
matter
within
cavity,
subtle
changes
resazurin
concentration
during
reaction
can
be
translated
into
detectable
wavelength
shifts
spectrum.
With
narrow
peaks,
sensing
resolution
reach
down
30
pM
per
10
pm
shift.
Combined
with
scanning
platform,
mapped
intercellular
heterogeneities
metabolism.
Further
applications
identification,
oxidative
stress
assessment,
drug
evaluation
revealed
universal
applicability
method
assays
biomedical
analysis,
providing
insights
disease
diagnosis
screening.
Analytical Chemistry,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 2, 2025
Spatial
metabolomics
based
on
mass
spectrometry
imaging
(MSI)
is
a
promising
approach
for
fundamental
biological
research
and
disease
biomarker
discovery.
It
simultaneously
reveals
the
spatial
distributions
of
hundreds
metabolites
across
tissue
sections.
While
previous
MSI
experiments
predominantly
rely
high-resolution
analysis
metabolite
annotation,
high
specificity
in
resolving
molecular
structures
essential
to
distinguish
isomers
or
isobars
obtain
ultimate
identities
metabolites.
This
also
critical
correlating
their
functions
with
distribution
patterns.
Tandem
(MS/MS)
effectively
used
structural
information
has
been
integrated
into
mapping
structurally
distinct
biomolecules,
though
typically
low
coverage.
The
main
technical
challenge
achieving
high-coverage,
high-structure-resolving
biomolecules
lies
limited
amount
sample
available
from
each
pixel
conventional
MS/MS
analysis,
which
restricts
number
scans
that
can
be
conducted
precursors
interest.
In
this
Perspective,
we
highlight
recent
developments
advanced
strategies
aimed
at
high-coverage
metabolomics.
Analytical Chemistry,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 4, 2025
Tumor
microenvironment
(TME)
is
characterized
by
complex
cellular
composition
and
high
molecular
heterogeneity.
Characterizing
the
metabolic
interactions
between
different
cells
in
TME
important
for
understanding
signatures
of
tumors
identifying
potential
vulnerabilities
tumor
treatment.
In
this
research,
we
develop
a
single-cell
spatial
metabolomics
method
to
profile
cell-specific
cell-cell
using
matrix-assisted
laser
desorption/ionization
mass
spectrometry
imaging
(MALDI-MSI).
Different
low-molecular-weight
metabolites
lipids
including
glutamate,
aspartate,
glutamine,
taurine,
phenylalanine,
glutathione,
fatty
acids,
phospholipids,
etc.
were
successfully
detected
imaged
after
optimizing
cell
culture
conductive
slides,
washing,
fixation
procedures.
Subsequently,
carried
out
on
H460
large-cell
lung
cancer
cells,
HT-29
colorectal
A549
HUH-7
liver
cancer-fibroblasts
coculture
system.
We
revealed
that
profiles
both
fibroblasts
altered
coculture.
Glutamate
aspartate
significantly
increased
with
corresponding
their
indispensable
roles
creation
pro-cancer
microenvironment.
addition,
discovered
expressions
acids
phospholipids
also
changed
coculture,
which
closely
related
competition
energy
nutrient
cells.
anticipate
analysis
be
broadly
used
investigations
diverse
models
interactions.
Abstract
Here
we
show
that
a
recently
developed
single
cell
mass
spectrometry
method
can
be
used
to
monitor
the
incorporation
of
an
isotopically
labeled
precursor
into
plant
protoplasts.
Specifically,
deuterium-labeled
tryptamine
alkaloid
pathway
over
course
24
hours.
The
resulting
data
provides
glimpse
rate
synthesis
and
transport
chemically
complex
monoterpene
indole
alkaloids
in
cells
across
small
population.
By
measuring
concentration
alkaloids,
gain
insight
flux
important
biosynthetic
pathway.
Stable-isotope
labeling
is
widely
approach
study
metabolic
networks
by
tracking
isotopologues
time.
This
manuscript
proof
principle
isotopic
performed
pathways.
Journal of Proteome Research,
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 22, 2024
Recent
advancements
in
single-cell
(sc)
resolution
analyses,
particularly
sc
transcriptomics
and
proteomics,
have
revolutionized
our
ability
to
probe
understand
cellular
heterogeneity.
The
study
of
metabolism
through
small
molecules,
metabolomics,
provides
an
additional
level
information
otherwise
unattainable
by
or
proteomics
shedding
light
on
the
metabolic
pathways
that
translate
gene
expression
into
functional
outcomes.
Metabolic
heterogeneity,
critical
health
disease,
impacts
developmental
outcomes,
disease
progression,
treatment
responses.
However,
dedicated
approaches
probing
metabolome
not
reached
maturity
other
omics
technologies.
Over
past
decade,
innovations
metabolomics
addressed
some
practical
limitations,
including
cell
isolation,
signal
sensitivity,
throughput.
To
fully
exploit
their
potential
biological
research,
however,
remaining
challenges
must
be
thoroughly
addressed.
Additionally,
integrating
with
orthogonal
techniques
will
required
validate
relevant
results
gain
systems-level
understanding.
This
perspective
offers
a
broad-stroke
overview
recent
mass
spectrometry
(MS)-based
advancements,
focusing
ongoing
from
biologist's
viewpoint,
aimed
at
addressing
pertinent
innovative
questions.
we
emphasize
use
showcase
systems
these
sophisticated
methodologies
are
apt
explore.
Summary
Single-cell
metabolomics
promises
to
resolve
metabolic
cellular
heterogeneity,
yet
current
methods
struggle
with
detecting
small
molecules,
throughput,
and
reproducibility.
Addressing
these
gaps,
we
developed
HT
SpaceM,
a
high-throughput
single-cell
method
novel
cell
preparation,
custom
glass
slides,
small-molecule
MALDI
imaging
mass
spectrometry
protocol,
batch
processing.
We
propose
unified
framework
covering
essential
data
analysis
steps
including
quality
control,
characterization,
differential
analysis,
structural
validation
functional
analysis.
Interrogating
human
HeLa
mouse
NIH3T3
cells,
detected
73
diverse
metabolites
validated
by
bulk
LC-MS/MS,
achieving
high
reproducibility
across
wells
slides.
nine
NCI-60
cancer
cells
HeLa,
identified
cell-type
markers
in
subpopulations.
Functional
revealed
overrepresented
pathways,
co-abundant
metabolites,
hubs.
demonstrate
the
ability
of
SCM
analyze
over
120,000
from
112
samples,
provide
guidance
interpret
revealing
insights
beyond
population
averages.
