18 research outputs found
Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia
Abstract In addition to being causally linked to the formation of multiple tumor types, tobacco use has been associated with decreased efficacy of anticancer treatment and reduced survival time. A detailed understanding of the cellular mechanisms that are affected by tobacco smoke (TS) should facilitate the development of improved preventive and therapeutic strategies. We have investigated the effects of a TS extract on the transcriptome of MSK-Leuk1 cells, a cellular model of oral leukoplakia. Using Affymetrix HGU133 Plus 2 arrays, 411 differentially expressed probe sets were identified. The observed transcriptome changes were grouped according to functional information and translated into molecular interaction network maps and signaling pathways. Pathways related to cellular proliferation, inflammation, apoptosis, and tissue injury seemed to be perturbed. Analysis of networks connecting the affected genes identified specific modulated molecular interactions, hubs, and key transcription regulators. Thus, TS was found to induce several epidermal growth factor receptor (EGFR) ligands forming an EGFR-centered molecular interaction network, as well as several aryl hydrocarbon receptor-dependent genes, including the xenobiotic metabolizing enzymes CYP1A1 and CYP1B1. Notably, the latter findings in vitro are consistent with our parallel finding that CYP1A1 and CYP1B1 levels were increased in oral mucosa of smokers. Collectively, these results offer insights into the mechanisms underlying the procarcinogenic effects of TS and raise the possibility that inhibitors of EGFR or aryl hydrocarbon receptor signaling will prevent or delay the development of TS-related tumors. Moreover, the inductive effects of TS on xenobiotic metabolizing enzymes may help explain the reduced efficacy of chemotherapy, and suggest targets for chemopreventive agents in smokers
Advances in structure elucidation of small molecules using mass spectrometry
The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules
Identification of common genetic risk variants for autism spectrum disorder
Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample-size increase from a unique Danish population resource, we report a genome-wide association meta-analysis of 18,381 individuals with ASD and 27,969 controls that identified five genome-wide-significant loci. Leveraging GWAS results from three phenotypes with significantly overlapping genetic architectures (schizophrenia, major depression, and educational attainment), we identified seven additional loci shared with other traits at equally strict significance levels. Dissecting the polygenic architecture, we found both quantitative and qualitative polygenic heterogeneity across ASD subtypes. These results highlight biological insights, particularly relating to neuronal function and corticogenesis, and establish that GWAS performed at scale will be much more productive in the near term in ASD
Gene expression imputation across multiple brain regions provides insights into schizophrenia risk
Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression
Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes
publisher: Elsevier articletitle: Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes journaltitle: Cell articlelink: https://doi.org/10.1016/j.cell.2018.05.046 content_type: article copyright: © 2018 Elsevier Inc
Reprogramming a DNA methylation mutant
Chemical
modification
of
the
cytosine
base
via
the
addition
of
a
methyl
group
to
form
5-‐methylcytosine
(5-‐mC)
is
a
well-‐studied
example
of
an
epigenetic
mark,
which
contributes
to
regulation
of
gene
expression,
chromatin
organisation
and
other
such
cellular
processes
without
affecting
the
underlying
DNA
sequence.
In
recent
years
it
was
shown
that
5-‐mC
is
not
the
only
DNA
modification
found
within
the
vertebrate
genome.
5-‐hydroxymethylcytosine
(5-‐hmC)
was
first
described
in
1952
although
it
wasn’t
until
2009
when
it
was
rediscovered
in
mammalian
tissues
that
it
sparked
intense
interest
in
the
field.
Research
has
found
that
unlike
the
5-‐mC
base
from
which
it
is
derived,
5-‐hmC
displays
variable
levels
and
patterns
across
a
multitude
of
tissue
and
cell
types.
As
such
the
patterns
of
these
DNA
modifications
can
act
as
an
identifier
of
cell
state.
This
thesis
aims
to
characterize
the
methyl
and
hydroxymethyl
profiles
of
induced
pluripotent
stem
cells
(iPSCs),
derived
from
control
mouse
embryonic
fibroblast
cell
line
(p53-‐/-‐)
as
well
as
and
methylation
hypomorphic
(p53-‐/-‐,
Dnmt1
-‐/-‐)
mutant
cell
lines.
As
such
both
somatic
cells
were
subject
to
reprogramming
with
Yamanaka
factors
(Oct4,
cMyc,
Klf4
and
Sox2)
via
the
piggyback
transposition
technique.
Successful
reprogramming
was
confirmed
by
a
number
of
techniques
and
outcomes,
including
the
de
novo
expression
of
a
number
of
key
pluripotency
related
factors
(Nanog,
Sall4
and
Gdf3).
Reprogrammed
cells
were
then
analysed
for
transcriptomic
changes
as
well
as
alterations
to
their
methyl
and
hydroxymethyl
landscapes
that
accompany
reprogramming.
Through
this
work
I
have
shown
that
the
reprogramming
of
MEF
derived
cell
lines
results
in
a
global
increase
in
5-‐hmC
for
both
p53-‐/-‐
and
(p53-‐/-‐,
Dnmt1
-‐/-‐)
hypomorphic
mutant
cell
lines
–
possibly
through
the
reactivation
of
an
alternative
form
of
DNMT1.
I
demonstrate
by
both
antibody
based
dot
blot
assay
and
genome
wide
sequencing
that
the
reprogramming
of
the
(p53-‐/-‐,
Dnmt1
-‐/-‐)
somatic
cells
towards
a
pluripotent
state
brings
about
an
increase
in
methylation
levels
within
the
cells.
This
latter
observation
may
indicate
that
the
reprogramming
of
the
cells
is
driving
them
towards
a
more
wild
type
phenotypic
state.
My
studies
suggest
that
lack
of
DNMT1
function
is
not
a
barrier
to
reprogramming
of
somatic
cells