Trends in biotechnology,
Journal Year:
2021,
Volume and Issue:
40(6), P. 647 - 676
Published: Dec. 28, 2021
Tumors
are
unique
and
complex
ecosystems,
in
which
heterogeneous
cell
subpopulations
with
variable
molecular
profiles,
aggressiveness,
proliferation
potential
coexist
interact.
Understanding
how
heterogeneity
influences
tumor
progression
has
important
clinical
implications
for
improving
diagnosis,
prognosis,
treatment
response
prediction.
Several
recent
innovations
data
acquisition
methods
computational
metrics
have
enabled
the
quantification
of
spatiotemporal
across
different
scales
organization.
Here,
we
summarize
most
promising
efforts
from
a
common
experimental
perspective,
discussing
their
advantages,
shortcomings,
challenges.
With
personalized
medicine
entering
new
era
unprecedented
opportunities,
our
vision
is
that
future
workflows
integrating
modalities,
scales,
dimensions
to
capture
intricate
aspects
ecosystem
open
avenues
improved
patient
care.
Cell Reports,
Journal Year:
2021,
Volume and Issue:
37(5), P. 109915 - 109915
Published: Nov. 1, 2021
Single-cell
RNA
sequencing
has
revealed
extensive
molecular
diversity
in
gene
programs
governing
mammalian
spermatogenesis
but
fails
to
delineate
their
dynamics
the
native
context
of
seminiferous
tubules,
spatially
confined
functional
units
spermatogenesis.
Here,
we
use
Slide-seq,
a
spatial
transcriptomics
technology,
generate
an
atlas
that
captures
expression
patterns
at
near-single-cell
resolution
mouse
and
human
testis.
Using
Slide-seq
data,
devise
computational
framework
accurately
localizes
testicular
cell
types
individual
tubules.
Unbiased
analysis
systematically
identifies
patterned
genes
programs.
Combining
with
targeted
situ
sequencing,
demonstrate
significant
differences
cellular
compositions
spermatogonial
microenvironment
between
testes.
Finally,
comparison
generated
from
wild-type
diabetic
testis
reveals
disruption
organization
tubules
as
potential
mechanism
diabetes-induced
male
infertility.
The Journal of Chemical Physics,
Journal Year:
2021,
Volume and Issue:
155(1)
Published: July 1, 2021
Three-dimensional
(3D)
organization
of
the
human
genome
plays
an
essential
role
in
all
DNA-templated
processes,
including
gene
transcription,
regulation,
and
DNA
replication.
Computational
modeling
can
be
effective
way
building
high-resolution
structures
improving
our
understanding
these
molecular
processes.
However,
it
faces
significant
challenges
as
consists
over
6
×
10
Trends in biotechnology,
Journal Year:
2021,
Volume and Issue:
40(6), P. 647 - 676
Published: Dec. 28, 2021
Tumors
are
unique
and
complex
ecosystems,
in
which
heterogeneous
cell
subpopulations
with
variable
molecular
profiles,
aggressiveness,
proliferation
potential
coexist
interact.
Understanding
how
heterogeneity
influences
tumor
progression
has
important
clinical
implications
for
improving
diagnosis,
prognosis,
treatment
response
prediction.
Several
recent
innovations
data
acquisition
methods
computational
metrics
have
enabled
the
quantification
of
spatiotemporal
across
different
scales
organization.
Here,
we
summarize
most
promising
efforts
from
a
common
experimental
perspective,
discussing
their
advantages,
shortcomings,
challenges.
With
personalized
medicine
entering
new
era
unprecedented
opportunities,
our
vision
is
that
future
workflows
integrating
modalities,
scales,
dimensions
to
capture
intricate
aspects
ecosystem
open
avenues
improved
patient
care.
