Stem Cell Reports,
Journal Year:
2023,
Volume and Issue:
18(6), P. 1255 - 1270
Published: June 1, 2023
In
the
past
decade,
term
organoid
has
moved
from
obscurity
to
common
use
describe
a
3D
in
vitro
cellular
model
of
tissue
that
recapitulates
structural
and
functional
elements
vivo
organ
it
models.
The
is
now
applied
structures
formed
as
result
two
distinct
processes:
capacity
for
adult
epithelial
stem
cells
re-create
niche
ability
direct
differentiation
pluripotent
self-organizing
multicellular
organogenesis.
While
these
fields
rely
upon
different
cell
types
recapitulate
processes,
both
share
challenges
around
robustness,
accuracy,
reproducibility.
Critically,
organoids
are
not
organs.
This
commentary
serves
discuss
challenges,
how
they
impact
genuine
utility,
shine
light
on
need
improve
standards
all
approaches.
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.
Annual Review of Immunology,
Journal Year:
2024,
Volume and Issue:
42(1), P. 207 - 233
Published: Jan. 12, 2024
The
immune
system
and
the
kidneys
are
closely
related.
Immune
components
mediate
acute
kidney
disease
crucial
to
progression
of
chronic
disease.
Beyond
its
pathogenic
functions,
supports
immunological
homeostasis
in
healthy
kidneys.
help
maintain
equilibrium
by
removing
metabolic
waste
products
toxins,
thereby
limiting
local
systemic
inflammation.
In
this
review,
we
describe
close
relationship
between
We
discuss
how
imbalance
response
can
be
deleterious
immunomodulation
important
preventing
end-stage
renal
addition,
recent
tools
such
as
silico
platforms
organoids
unveil
cells
homeostasis.
Nature Methods,
Journal Year:
2024,
Volume and Issue:
21(10), P. 1796 - 1800
Published: Aug. 29, 2024
The
integration
of
spatial
omics
technologies
can
provide
important
insights
into
the
biology
tissues.
Here
we
combined
mass
spectrometry
imaging-based
metabolomics
and
imaging
cytometry-based
immunophenotyping
on
a
single
tissue
section
to
reveal
metabolic
heterogeneity
at
single-cell
resolution
within
tissues
its
association
with
specific
cell
populations
such
as
cancer
cells
or
immune
cells.
This
approach
has
potential
greatly
increase
our
understanding
tissue-level
interplay
between
processes
their
cellular
components.
authors
present
workflow
integrating
cytometry
deconvolute
level.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: May 13, 2024
Abstract
The
growing
disparity
between
the
demand
for
transplants
and
available
donor
supply,
coupled
with
an
aging
population
increasing
prevalence
of
chronic
diseases,
highlights
urgent
need
development
platforms
enabling
reconditioning,
repair,
regeneration
deceased
organs.
This
necessitates
ability
to
preserve
metabolically
active
kidneys
ex
vivo
days.
However,
current
kidney
normothermic
machine
perfusion
(NMP)
approaches
allow
metabolic
preservation
only
hours.
Here
we
show
that
human
discarded
transplantation
can
be
preserved
in
a
state
up
4
days
when
perfused
cell-free
perfusate
supplemented
TCA
cycle
intermediates
at
subnormothermia
(25
°C).
Using
spatially
resolved
isotope
tracing
demonstrate
fluxes
microenvironment
Day
perfusion.
Beyond
4,
significant
changes
were
observed
renal
cell
populations
through
spatial
lipidomics,
increases
injury
markers
such
as
LDH,
NGAL
oxidized
lipids.
Finally,
maintain
functional
parameters
4.
Collectively,
these
findings
provide
evidence
this
approach
enables
over
multiple
days,
establishing
solid
foundation
future
clinical
investigations.
Briefings in Bioinformatics,
Journal Year:
2024,
Volume and Issue:
25(5)
Published: July 25, 2024
The
development
of
omics
technologies
has
driven
a
profound
expansion
in
the
scale
biological
data
and
increased
complexity
internal
dimensions,
prompting
utilization
machine
learning
(ML)
as
powerful
toolkit
for
extracting
knowledge
understanding
underlying
patterns.
Kidney
disease
represents
one
major
growing
global
health
threats
with
intricate
pathogenic
mechanisms
lack
precise
molecular
pathology-based
therapeutic
modalities.
Accordingly,
there
is
need
advanced
high-throughput
approaches
to
capture
implicit
features
complement
current
experiments
statistics.
This
review
aims
delineate
strategies
integrating
multi-omics
appropriate
ML
methods,
highlighting
key
clinical
translational
scenarios,
including
predicting
progression
risks
improve
medical
decision-making,
comprehensively
mechanisms,
practical
applications
image
recognition
renal
digital
pathology.
Examining
benefits
challenges
integration
efforts
expected
shed
light
on
kidney
advance
practice.
