Frontiers in Genome Editing,
Год журнала:
2024,
Номер
6
Опубликована: Окт. 31, 2024
Large
scale
cancer
genomic
studies
in
patients
have
unveiled
millions
of
non-coding
variants.
While
a
handful
been
shown
to
drive
development,
the
vast
majority
unknown
function.
This
review
describes
challenges
functionally
annotating
variants
and
understanding
how
they
contribute
cancer.
We
summarize
recently
developed
high-throughput
technologies
address
these
challenges.
Finally,
we
outline
future
prospects
for
genetics
help
catalyze
personalized
therapy.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Март 27, 2024
Prime
editing
installs
precise
edits
into
the
genome
with
minimal
unwanted
byproducts,
but
low
and
variable
efficiencies
have
complicated
application
of
approach
to
high-throughput
functional
genomics.
Leveraging
several
recent
advances,
we
assembled
a
prime
platform
capable
high-efficiency
substitution
across
set
engineered
guide
RNAs
(epegRNAs)
corresponding
target
sequences
(80%
median
intended
editing).
Then,
using
custom
library
240,000
epegRNAs
targeting
>17,000
codons
175
different
types,
benchmarked
our
for
interrogation
small
variants
(1-3
nucleotides)
targeted
essential
genes.
Resulting
data
identified
negative
growth
phenotypes
nonsense
mutations
~8,000
codons,
comparing
those
results
from
controls
demonstrated
high
specificity.
We
also
observed
synonymous
that
disrupted
splice
site
motifs
at
3'
exon
boundaries.
Altogether,
establish
benchmark
characterization
genetic
simple
readouts
multiplexed
experiments.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июнь 1, 2024
Abstract
Genomic
variation
ranging
from
single
nucleotide
polymorphisms
to
structural
variants
can
impact
gene
function
and
expression,
contributing
disease
mechanisms
such
as
cancer
progression.
The
systematic
study
of
this
is
hindered
by
inefficient
precision
editing
tools
making
it
challenging
confidently
link
genotype
expression
in
pooled
screens.
Additionally,
assessing
heterogenous
primary
tumor
samples
at
scale
difficult
with
current
single-cell
technologies.
We
developed
droplet-based
multiomic
targeted
scDNA-scRNAseq
(SDR-seq)
precisely
genotypes
profiles
high-throughput.
SDR-seq
simultaneously
assesses
up
480
RNA
gDNA
targets
high
coverage
sensitivity
across
thousands
cells.
Using
SDR-seq,
we
associate
coding
non-coding
distinct
human
iPSCs.
Furthermore,
demonstrate
that
B-cell
lymphoma
samples,
cells
a
higher
mutational
burden
exhibit
elevated
receptor
signaling
tumorigenic
expression.
has
broad
potential
for
gaining
functional
insights
into
regulatory
encoded
genetic
diverse
loci,
advancing
our
ability
regulation
its
implications
disease.
Cell Genomics,
Год журнала:
2024,
Номер
4(9), С. 100630 - 100630
Опубликована: Авг. 13, 2024
Raynaud's
syndrome
is
a
dysautonomia
where
exposure
to
cold
causes
vasoconstriction
and
hypoxia,
particularly
in
the
extremities.
We
performed
meta-analysis
four
cohorts
discovered
eight
loci
(ADRA2A,
IRX1,
NOS3,
ACVR2A,
TMEM51,
PCDH10-DT,
HLA,
RAB6C)
ADRA2A,
IRX1
co-localized
with
expression
quantitative
trait
(eQTLs),
distal
arteries.
CRISPR
gene
editing
further
showed
that
ADRA2A
NOS3
modified
situ
RNAscope
clarified
specificity
of
small
vessels
around
capillaries
skin.
A
functional
contraction
assay
lower
ADRA2A-deficient
higher
ADRA2A-overexpressing
smooth
muscle
cells.
Overall,
our
study
highlights
power
genome-wide
association
testing
follow-up
as
method
understand
complex
diseases.
The
results
indicate
temperature-dependent
adrenergic
signaling
through
effects
at
microvasculature
by
endothelial
immune
mechanisms
HLA
locus
syndrome.
Frontiers in Genome Editing,
Год журнала:
2024,
Номер
6
Опубликована: Окт. 31, 2024
Large
scale
cancer
genomic
studies
in
patients
have
unveiled
millions
of
non-coding
variants.
While
a
handful
been
shown
to
drive
development,
the
vast
majority
unknown
function.
This
review
describes
challenges
functionally
annotating
variants
and
understanding
how
they
contribute
cancer.
We
summarize
recently
developed
high-throughput
technologies
address
these
challenges.
Finally,
we
outline
future
prospects
for
genetics
help
catalyze
personalized
therapy.
