bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: April 2, 2024
The
Human
BioMolecular
Atlas
Program
(HuBMAP)
aims
to
construct
a
reference
3D
structural,
cellular,
and
molecular
atlas
of
the
healthy
adult
human
body.
HuBMAP
Data
Portal
(https://portal.hubmapconsortium.org)
serves
experimental
datasets
supports
data
processing,
search,
filtering,
visualization.
Reference
(HRA)
(https://humanatlas.io)
provides
open
access
data,
code,
procedures,
instructional
materials.
Experts
from
more
than
20
consortia
are
collaborating
HRA's
Common
Coordinate
Framework
(CCF),
knowledge
graphs,
tools
that
describe
multiscale
structure
body
(from
organs
tissues
down
cells,
genes,
biomarkers)
use
HRA
understand
changes
occur
at
each
these
levels
with
aging,
disease,
other
perturbations.
6th
release
v2.0
covers
36
4,499
unique
anatomical
structures,
1,195
cell
types,
2,089
biomarkers
(e.g.,
proteins,
lipids)
linked
ontologies
2D/3D
objects.
New
can
be
mapped
into
using
(1)
three
type
annotation
Azimuth)
or
(2)
validated
antibody
panels
(OMAPs),
(3)
by
registering
tissue
spatially.
This
paper
describes
user
stories,
terminology,
formats,
ontology
validation,
unified
analysis
workflows,
interfaces,
materials,
application
programming
interface
(APIs),
flexible
hybrid
cloud
infrastructure,
previews
usage
applications.
Signal Transduction and Targeted Therapy,
Journal Year:
2024,
Volume and Issue:
9(1)
Published: Feb. 16, 2024
Abstract
The
human
gastrointestinal
tract
is
populated
with
a
diverse
microbial
community.
vast
genetic
and
metabolic
potential
of
the
gut
microbiome
underpins
its
ubiquity
in
nearly
every
aspect
biology,
including
health
maintenance,
development,
aging,
disease.
advent
new
sequencing
technologies
culture-independent
methods
has
allowed
researchers
to
move
beyond
correlative
studies
toward
mechanistic
explorations
shed
light
on
microbiome–host
interactions.
Evidence
unveiled
bidirectional
communication
between
central
nervous
system,
referred
as
“microbiota–gut–brain
axis”.
microbiota–gut–brain
axis
represents
an
important
regulator
glial
functions,
making
it
actionable
target
ameliorate
development
progression
neurodegenerative
diseases.
In
this
review,
we
discuss
mechanisms
As
provides
essential
cues
microglia,
astrocytes,
oligodendrocytes,
examine
communications
microbiota
these
cells
during
healthy
states
Subsequently,
diseases
using
metabolite-centric
approach,
while
also
examining
role
microbiota-related
neurotransmitters
hormones.
Next,
targeting
intestinal
barrier,
blood–brain
meninges,
peripheral
immune
system
counteract
dysfunction
neurodegeneration.
Finally,
conclude
by
assessing
pre-clinical
clinical
evidence
probiotics,
prebiotics,
fecal
transplantation
A
thorough
comprehension
will
foster
effective
therapeutic
interventions
for
management
Cell,
Journal Year:
2024,
Volume and Issue:
187(10), P. 2485 - 2501.e26
Published: April 22, 2024
Glioma
contains
malignant
cells
in
diverse
states.
Here,
we
combine
spatial
transcriptomics,
proteomics,
and
computational
approaches
to
define
glioma
cellular
states
uncover
their
organization.
We
find
three
prominent
modes
of
First,
gliomas
are
composed
small
local
environments,
each
typically
enriched
with
one
major
state.
Second,
specific
pairs
preferentially
reside
proximity
across
multiple
scales.
This
pairing
is
consistent
tumors.
Third,
these
pairwise
interactions
collectively
a
global
architecture
five
layers.
Hypoxia
appears
drive
the
layers,
as
it
associated
long-range
organization
that
includes
all
cancer
cell
Accordingly,
tumor
regions
distant
from
any
hypoxic/necrotic
foci
tumors
lack
hypoxia
such
low-grade
IDH-mutant
less
organized.
In
summary,
provide
conceptual
framework
for
glioma,
highlighting
tissue
organizer.
Nature Genetics,
Journal Year:
2024,
Volume and Issue:
56(3), P. 431 - 441
Published: Feb. 27, 2024
Spatial
omics
data
are
clustered
to
define
both
cell
types
and
tissue
domains.
We
present
Building
Aggregates
with
a
Neighborhood
Kernel
Yardstick
(BANKSY),
an
algorithm
that
unifies
these
two
spatial
clustering
problems
by
embedding
cells
in
product
space
of
their
own
the
local
neighborhood
transcriptome,
representing
state
microenvironment,
respectively.
BANKSY's
feature
augmentation
strategy
improved
performance
on
tasks
when
tested
diverse
RNA
(imaging,
sequencing)
protein
(imaging)
datasets.
BANKSY
revealed
unexpected
niche-dependent
states
mouse
brain
outperformed
competing
methods
domain
segmentation
typing
benchmarks.
can
also
be
used
for
quality
control
transcriptomics
spatially
aware
batch
effect
correction.
Importantly,
it
is
substantially
faster
more
scalable
than
existing
methods,
enabling
processing
millions
In
summary,
provides
accurate,
biologically
motivated,
versatile
framework
analyzing
resolved
data.
Cancer Discovery,
Journal Year:
2024,
Volume and Issue:
14(8), P. 1418 - 1439
Published: March 27, 2024
Abstract
Tumor-associated
macrophages
are
transcriptionally
heterogeneous,
but
the
spatial
distribution
and
cell
interactions
that
shape
macrophage
tissue
roles
remain
poorly
characterized.
Here,
we
spatially
resolve
five
distinct
human
populations
in
normal
malignant
breast
colon
reveal
their
cellular
associations.
This
map
reveals
reside
segregated
micro-environmental
niches
with
conserved
compositions
repeated
across
healthy
diseased
tissue.
We
show
IL4I1+
phagocytose
dying
cells
areas
high
turnover
predict
good
outcome
cancer.
In
contrast,
SPP1+
enriched
hypoxic
necrotic
tumor
regions
portend
worse
A
subset
of
FOLR2+
is
embedded
plasma
niches.
NLRP3+
co-localize
neutrophils
activate
an
inflammasome
tumors.
Our
findings
indicate
a
limited
number
unique
function
as
fundamental
building
blocks
Significance:
work
broadens
our
understanding
different
may
exert
on
cancer
growth
potential
predictive
markers
population-specific
therapy
targets.
