Nucleic Acids Research,
Год журнала:
2024,
Номер
52(W1), С. W398 - W406
Опубликована: Апрель 8, 2024
Abstract
We
introduce
MetaboAnalyst
version
6.0
as
a
unified
platform
for
processing,
analyzing,
and
interpreting
data
from
targeted
well
untargeted
metabolomics
studies
using
liquid
chromatography
-
mass
spectrometry
(LC–MS).
The
two
main
objectives
in
developing
are
to
support
tandem
MS
(MS2)
processing
annotation,
the
analysis
of
exposomics
related
experiments.
Key
features
include:
(i)
significantly
enhanced
Spectra
Processing
module
with
MS2
asari
algorithm;
(ii)
Peak
Annotation
based
on
comprehensive
reference
databases
fragment-level
annotation;
(iii)
new
Statistical
Analysis
dedicated
handling
complex
study
design
multiple
factors
or
phenotypic
descriptors;
(iv)
Causal
estimating
metabolite
phenotype
causal
relations
two-sample
Mendelian
randomization,
(v)
Dose-Response
benchmark
dose
calculations.
In
addition,
we
have
also
improved
MetaboAnalyst's
visualization
functions,
updated
its
compound
database
sets,
expanded
pathway
around
130
species.
is
freely
available
at
https://www.metaboanalyst.ca.
Signal Transduction and Targeted Therapy,
Год журнала:
2023,
Номер
8(1)
Опубликована: Март 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.
Multi-omics
usually
refers
to
the
crossover
application
of
multiple
high-throughput
screening
technologies
represented
by
genomics,
transcriptomics,
single-cell
proteomics
and
metabolomics,
spatial
so
on,
which
play
a
great
role
in
promoting
study
human
diseases.
Most
current
reviews
focus
on
describing
development
multi-omics
technologies,
data
integration,
particular
disease;
however,
few
them
provide
comprehensive
systematic
introduction
multi-omics.
This
review
outlines
existing
technical
categories
multi-omics,
cautions
for
experimental
design,
focuses
integrated
analysis
methods
especially
approach
machine
learning
deep
integration
corresponding
tools,
medical
researches
(e.g.,
cancer,
neurodegenerative
diseases,
aging,
drug
target
discovery)
as
well
open-source
tools
databases,
finally,
discusses
challenges
future
directions
precision
medicine.
With
algorithms,
important
disease
research,
also
provided
detailed
introduction.
will
guidance
researchers,
who
are
just
entering
into
research.
Briefings in Bioinformatics,
Год журнала:
2022,
Номер
24(1)
Опубликована: Ноя. 15, 2022
Global
or
untargeted
metabolomics
is
widely
used
to
comprehensively
investigate
metabolic
profiles
under
various
pathophysiological
conditions
such
as
inflammations,
infections,
responses
exposures
interactions
with
microbial
communities.
However,
biological
interpretation
of
global
data
remains
a
daunting
task.
Recent
years
have
seen
growing
applications
pathway
enrichment
analysis
based
on
putative
annotations
liquid
chromatography
coupled
mass
spectrometry
(LC-MS)
peaks
for
functional
LC-MS-based
data.
due
intricate
peak-metabolite
and
metabolite-pathway
relationships,
considerable
variations
are
observed
among
results
obtained
using
different
approaches.
There
an
urgent
need
benchmark
these
approaches
inform
the
best
practices.We
conducted
study
common
peak
annotation
methods
in
current
studies.
Representative
approaches,
including
three
four
methods,
were
selected
benchmarked
scenarios.
Based
results,
we
provided
set
recommendations
regarding
annotation,
ranking
metrics
feature
selection.
The
overall
better
performance
was
mummichog
approach.
We
that
~30%
rate
sufficient
achieve
high
recall
(~90%
mummichog),
semi-annotated
improves
interpretation.
platforms
further
propose
identifiability
index
indicate
possibility
being
reliably
identified.
Finally,
evaluated
all
11
COVID-19
8
inflammatory
bowel
diseases
(IBD)
datasets.
Cell Host & Microbe,
Год журнала:
2023,
Номер
31(6), С. 1038 - 1053.e10
Опубликована: Июнь 1, 2023
The
microbes
and
microbial
pathways
that
influence
host
inflammatory
disease
progression
remain
largely
undefined.
Here,
we
show
variation
in
atherosclerosis
burden
is
partially
driven
by
gut
microbiota
associated
with
circulating
levels
of
uric
acid
(UA)
mice
humans.
We
identify
bacterial
taxa
spanning
multiple
phyla,
including
Bacillota,
Fusobacteriota,
Pseudomonadota,
use
purines,
UA
as
carbon
energy
sources
anaerobically.
a
gene
cluster
encodes
key
steps
anaerobic
purine
degradation
widely
distributed
among
gut-dwelling
bacteria.
Furthermore,
colonization
gnotobiotic
purine-degrading
bacteria
modulates
other
purines
the
systemically.
Thus,
are
important
drivers
global
homeostasis
serum
levels,
catabolism
may
represent
mechanism
which
health.
Cell Metabolism,
Год журнала:
2024,
Номер
36(4), С. 745 - 761.e5
Опубликована: Апрель 1, 2024
There
is
considerable
heterogeneity
in
the
cardiometabolic
abnormalities
associated
with
obesity.
We
evaluated
multi-organ
system
metabolic
function
20
adults
metabolically
healthy
obesity
(MHO;
normal
fasting
glucose
and
triglycerides,
oral
tolerance,
intrahepatic
triglyceride
content,
whole-body
insulin
sensitivity),
unhealthy
(MUO;
prediabetes,
hepatic
steatosis,
resistance),
15
who
were
lean.
Compared
MUO,
people
MHO
had
(1)
altered
skeletal
muscle
biology
(decreased
ceramide
content
increased
expression
of
genes
involved
BCAA
catabolism
mitochondrial
structure/function);
(2)
adipose
tissue
inflammation
extracellular
matrix
remodeling
lipogenesis);
(3)
lower
24-h
plasma
glucose,
insulin,
non-esterified
fatty
acids,
triglycerides;
(4)
higher
adiponectin
PAI-1
concentrations;
(5)
decreased
oxidative
stress.
These
findings
provide
a
framework
potential
mechanisms
responsible
for
This
study
was
registered
at
ClinicalTrials.gov
(NCT02706262).
Cell,
Год журнала:
2024,
Номер
187(8), С. 1853 - 1873.e15
Опубликована: Апрель 1, 2024
This
study
has
followed
a
birth
cohort
for
over
20
years
to
find
factors
associated
with
neurodevelopmental
disorder
(ND)
diagnosis.
Detailed,
early-life
longitudinal
questionnaires
captured
infection
and
antibiotic
events,
stress,
prenatal
factors,
family
history,
more.
Biomarkers
including
cord
serum
metabolome
lipidome,
human
leukocyte
antigen
(HLA)
genotype,
infant
microbiota,
stool
were
assessed.
Among
the
16,440
Swedish
children
across
time,
1,197
developed
an
ND.
Significant
associations
emerged
future
ND
diagnosis
in
general
specific
subtypes,
spanning
intellectual
disability,
speech
disorder,
attention-deficit/hyperactivity
autism.
investigation
revealed
microbiome
connections
as
well
early
emerging
mood
gastrointestinal
problems.
The
findings
suggest
links
immunodysregulation
metabolism,
compounded
by
infection,
antibiotics.
convergence
of
biomarkers
risk
this
prospective,
on
large-scale
population
establishes
foundation
prediction
intervention
neurodevelopment.
