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Effects of noise on vascular function, oxidative stress, and inflammation: mechanistic insight from studies in mice.

TL;DR: A novel and unique aircraft noise stress model with increased blood pressure and vascular dysfunction associated with oxidative stress is established, enabling future studies of molecular mechanisms, mitigation strategies, and pharmacological interventions to protect from noise-induced vascular damage.
Abstract: Aims Epidemiological studies indicate that traffic noise increases the incidence of coronary artery disease, hypertension and stroke. The underlying mechanisms remain largely unknown. Field studies with nighttime noise exposure demonstrate that aircraft noise leads to vascular dysfunction, which is markedly improved by vitamin C, suggesting a key role of oxidative stress in causing this phenomenon. Methods and results We developed a novel animal model to study the vascular consequences of aircraft noise exposure. Peak sound levels of 85 and mean sound level of 72 dBA applied by loudspeakers for 4 days caused an increase in systolic blood pressure, plasma noradrenaline and angiotensin II levels and induced endothelial dysfunction. Noise increased eNOS expression but reduced vascular NO levels because of eNOS uncoupling. Noise increased circulating levels of nitrotyrosine, interleukine-6 and vascular expression of the NADPH oxidase subunit Nox2, nitrotyrosine-positive proteins and of endothelin-1. FACS analysis demonstrated an increase in infiltrated natural killer-cells and neutrophils into the vasculature. Equal mean sound pressure levels of white noise for 4 days did not induce these changes. Comparative Illumina sequencing of transcriptomes of aortic tissues from aircraft noise-treated animals displayed significant changes of genes in part responsible for the regulation of vascular function, vascular remodelling, and cell death. Conclusion We established a novel and unique aircraft noise stress model with increased blood pressure and vascular dysfunction associated with oxidative stress. This animal model enables future studies of molecular mechanisms, mitigation strategies, and pharmacological interventions to protect from noise-induced vascular damage.

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Effects of noise on vascular function, oxidative
stress, and inflammation: mechanistic insight
from studies in mice
Thomas Mu¨nzel
1,2
*, Andreas Daiber
1,2
, Sebastian Steven
1
, Lan P. Tran
1
,
Elisabeth Ullmann
1
, Sabine Kossmann
1
, Frank P. Schmidt
1
, Matthias Oelze
1
,
Ning Xia
3
, Huige Li
3
, Antonio Pinto
4
, Philipp Wild
2,4
, Kai Pies
5
, Erwin R. Schmidt
6
,
Steffen Rapp
6
, and Swenja Kro¨ ller-Scho¨n
1
1
Center for Cardiology, Cardiology I Laboratory of Molecular Cardiology, University Medical Center at the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131
Mainz, Germany;
2
German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main;
3
Department of Pharmacology;
4
Preventive Cardiology and Preventive
Medicine, Center for Cardiology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany;
5
Engineering Office for Noise Protection, Mainz,
Germany; and
6
Institute for Molecular Genetics, Johannes Gutenberg University, Mainz, Germany
Received 24 August 2016; revised 25 October 2016; editorial decision 23 January 2017; accepted 6 February 2017; online publis h-ahead-of-print 17 February 2017
See page 2850 for the editorial comment on this article (doi: 10.1093/eurheartj/ehx217)
Aims Epidemiological studies indicate that traffic noise increases the incidence of coronary artery disease, hypertension
and stroke. The underlying mechanisms remain largely unknown. Field studies with nighttime noise exposure dem-
onstrate that aircraft noise leads to vascular dysfunction, which is markedly improved by vitamin C, suggesting a
key role of oxidative stress in causing this phenomenon.
...................................................................................................................................................................................................
Methods
and results
We developed a novel animal model to study the vascular consequences of aircraft noise exposure. Peak sound
levels of 85 and mean sound level of 72 dBA applied by loudspeakers for 4 days caused an increase in systolic
blood pressure, plasma noradrenaline and angiotensin II levels and induced endothelial dysfunction. Noise increased
eNOS expression but reduced vascular NO levels because of eNOS uncoupling. Noise increased circulating levels
of nitrotyrosine, interleukine-6 and vascular expression of the NADPH oxidase subunit Nox2, nitrotyrosine-
positive proteins and of endothelin-1. FACS analysis demonstrated an increase in infiltrated natural killer-cells and
neutrophils into the vasculature. Equal mean sound pressure levels of white noise for 4 days did not induce these
changes. Comparative Illumina sequencing of transcriptomes of aortic tissues from aircraft noise-treated animals
displayed significant changes of genes in part responsible for the regulation of vascular function, vascular remodel-
ling, and cell death.
...................................................................................................................................................................................................
Conclusion
We established a novel and unique aircraft noise stress model with increased blood pressure and vascular dysfunc-
tion associated with oxidative stress. This animal model enables future studies of molecular mechanisms, mitigation
strategies, and pharmacological interventions to protect from noise-induced vascular damage.
䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏䊏
Keywords
Environmental stressor
Noise exposure
Endothelial dysfunction
Oxidative stress
eNOS uncou-
pling
NADPH oxidase
Vascular inflammation
* Corresponding author. Tel: þ49 6131 17 7250, Fax: þ49 6131 17 6615, Email: tmuenzel@uni-mainz.de
V
C
The Author 2017. Published by Oxford University Press on behalf of the European Society of Cardiology.
This is an Ope n Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/),
which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
journals.permissions@oup.com
European Heart Journal (2017) 38, 2838–2849
BASIC SCIENCE
doi:10.1093/eurheartj/ehx081
Hypertension
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Introduction
The health burden of environmental noise exposure has been in-
creasingly acknowledged. The World Health Organization (WHO)
estimates that each year almost 1 million disability adjusted life years
are lost due to noise exposure in the Western European population.
Epidemiological studies have demonstrated that traffic noise ex-
posure is associated with cardiovascular diseases such as hyperten-
sion, myocardial infarction, and stroke.
13
Noise is a non-specific
stressor that arouses the autonomic nervous system and endocrine
system. Chronic low levels of noise can cause disturbances of activity,
sleep, and communication leading to emotional responses such as an-
noyance and subsequent stress.
4,5
Chronic stress in turn has been
demonstrated to generate its own cardiovascular risk factors such as
increased blood pressure and dyslipidemia, increased blood viscosity
and blood glucose and activation of blood clotting factors in animal
models
6,7
and humans.
812
Persistent chronic noise exposure in-
creases the risk of cardiovascular and metabolic diseases such
as hypertension, coronary artery disease, diabetes, and stroke.
1317
A recent meta-analysis reported on a linear relationship between
exposure to transportation noise and the incidence of ischaemic
heart diseases, warranting further studies to understand the mechan-
istic basis of this association.
18
We recently studied the effects of nighttime aircraft noise on vas-
cular (endothelial) function in healthy subjects
19
and demonstrated
that nighttime noise dose-dependently impairs endothelial function,
disrupts sleep quality and tends to increase blood pressure.
Importantly, in a subgroup of subjects, vitamin C significantly im-
proved flow-mediated dilation (FMD) suggesting that increased pro-
duction of reactive oxygen species (ROS) in response to noise
exposure contributes to vascular dysfunction.
19
In our subsequent
clinical study, we reported on synergistic adverse cardiovascular ef-
fects of noise exposure in patients with pre-established cardiovascu-
lar diseases, further supporting the role of oxidative stress.
20
Since previous animal models employed high dBA levels (up to
100 dBA),
2123
which can lead to direct auditory damage, we de-
veloped a novel noise exposure model in mice (C57Bl/6j) with lower
peak sound levels (<85 dBA), lower mean sound pressure levels (72
dBA) and shorter exposure times (1–4 days), which has been shown
to be safe and to cause mainly non-auditory effects to animals such as
stress reactions.
24
To our knowledge, no study has so far investigated
directly the vascular consequences of noise exposure. In the present
studies we sought to characterize the mechanisms of aircraft noise-
induced vascular (endothelial) dysfunction, e.g. to identify the sources
of ROS production, to assess the degree of imbalance of vascular
NO/O
:
2
-
production and the extent of inflammation in the vascula-
ture of noise-exposed animals. We also tested the consequences of
noise on the gene expression profile in the vasculature by performing
Illumina transcriptomic next generation sequencing.
Methods
Noise exposure
All animals were treated in accordance with the Guide for the Care
and Use of Laboratory Animals as adopted by the U.S. National
Institutes of Health and approval was granted by the Ethics
Committee of the University Medical Center Mainz and the
Landesuntersuchungsamt Rheinland-Pfalz (Koblenz, Germany; permit
number: 23 177-07/G 12-1-021 E3 and 23 177-07/G 15-1-094).
Noise exposure consisted of repetitive playbacks of a 2 hour long
noise pattern of 69 aircraft noise events with a duration of 43 s and a
maximum sound pressure level of 85 dB(A) and a mean sound pres-
sure level of 72 dB(A), which does not lead to hearing loss.
24
Noise
events were separated by silent periods with irregular distribution to
prevent early adaptation. The noise pattern was played back from
downward facing loudspeakers mounted approximately 30 cm above
the mouse cages with a Grundig MS 540 compact sound system with
a total output of 65 W. Loudness and corresponding sound pressure
levels were calibrated with a Class II Sound level meter (Casella CEL-
246) within one the cages at initial setup. Actual SPLs during expos-
ure was continuously recorded during the study period with the
same device placed between cages with upward facing microphone.
The average SPL (Leq3) is 72 dB(A) at a usual background noise level
of 48 dB(A) in the animal facility. In control experiments, mice were
exposed to ‘white noise (this is a random noise with constant spec-
tral density within the range of human hearing from 20 Hz to 20 kHz)
using exactly the same average SPL as for aircraft noise. All SPL and
maximum sound pressure levels were measured within the mouse
cages.
For further information of the methodology employed for deter-
mination of blood pressure, stress hormones, vascular function, nitric
oxide quantification, oxidative stress parameters, inflammatory path-
ways, gene and protein expression, next generation sequencing see
the Supplementary material online.
Results
Effects of noise exposure on laboratory
values, blood pressure and stress
hormone levels
Noise exposure for 1–4 days caused no significant changes in heart/
body weight ratio (Supplementary material online, Figure 1S). Blood
glucose levels were increased compared with controls during the en-
tire noise exposure period, while triglyceride levels were not
changed (Supplementary material online, Figure 1S). Four days of
noise exposure also increased systolic and mean blood pressure
(Figure
1A, C) while diastolic blood pressure did not change signifi-
cantly (Figure
1B). Plasma catecholamine levels (noradrenaline, dopa-
mine significantly and adrenaline by trend) and angiotensin II levels
increased (Figure
1D–G). Cortisol levels in urine showed no significant
change (although a trend for increased values in response to noise
exposure) and were increased in kidney after 4 days of noise expos-
ure (Figure
1H, I).
Effects of noise exposure on vascular
function
Noise exposure for 1, 2, and 4 days caused a significant attenuation of
ACh-induced relaxation of mouse aorta (Figure
2A, Supplementary
material online, Table 2S). Responses to the endothelium independ-
ent vasodilator GTN were also significantly modified (Figure 2B,
Supplementary material online,Table2S). Noise exposure induced an
Effects of noise on vascular function, oxidative stress, and inflammation 2839
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increase in sensitivity of the aorta to norepinephrine- and ET-1 medi-
ated vasoconstriction (Figure
2C, D, Supplementary material online,
Table 3S).
Effects of noise exposure on eNOS
expression, eNOS-mediated NO produc-
tion and the functionality of the NO/
cGMP signaling pathway
Endothelial dysfunction was paralleled by a decrease in vascular NO
production assessed by electron paramagnetic resonance (EPR)
(Figure
2E, F). Paradoxically, eNOS was up-regulated in vascular tissue
on day 4 of noise exposure (Figure
3A) and phosphorylation of eNOS
at Ser1177 was enhanced over the entire time period of noise expos-
ure (Figure
3B, C). Since eNOS-mediated NO production was
decreased despite up-regulation of eNOS expression and Ser1177
phosphorylation, we tested whether eNOS was uncoupled. Using
DHE staining vascular superoxide production was increased in ves-
sels from noise exposed animals and treatment with the eNOS inhibi-
tor L-NAME consistently decreased endothelial superoxide
production, identifying eNOS as a significant superoxide source
(Supplementary material online, Figure 2S). Noise causes S-glutathio-
nylation of eNOS, an established mechanism of eNOS uncoupling in
the aorta (Figure
3D) and the heart (Figure 4H). The expression of
GCH-1 and DHFR, both responsible for providing the eNOS cofac-
tor tetrahydrobiopterin (BH4), were up-regulated, compatible with a
counter regulatory response (Figure
3E, F).
With respect to the NO/cGMP/cGK-I signaling pathway, we did
not observe any changes in the expression of the sGC subunits
(Supplementary material online, Figure 3S). However in parallel to the
decrease in NO production on d1 we observed a decrease in the ac-
tivity of cGK-I as assessed by the diminished phosphorylation of the
VAsodilator-Stimulated Phosphoprotein at serine 239 (P-VASP)
(Supplementary material online, Figure 3S).
Figure 1 Effects of noise for 1, 2, and 4 days on blood pressure and stress hormone release. Noise increased significantly systolic and mean arterial
(A, C) but not diastolic (B) blood pressure. Noise increased noradrenalin, dopamine and angiotensin II levels significantly and adrenalin by trend
(DG). Cortisol levels in urine and kidney showed a weak trend for an increase under noise exposure, which was significant for kidney cortisol on day
4(H, I). Data are mean ± SD from n = 8–16 mice/day (A–C), 8–11 (D), 7–8 (E), 9–11 (F), 7–12 (G), 6–14 (H) and 7–12 (I) mice/group.
2840 T. Mu¨nzel et al.
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Effects of noise exposure on ROS
production in plasma, heart and the
vasculature
In plasma, noise exposure led to an increase in 3-nitrotyrosine-posi-
tive proteins (day 2–4), MDA-positive proteins (day 4) and interleu-
kin 6 (day 2–4) as established by Dot Blot measurements (Figure
4A–
C). In vascular tissue, noise exposure increased expression of the
NADPH oxidase subunit NOX-2 (day 1–4) and ET-1 (day 2), while
the NOX-1 subunit was not modified (Figure
4D–F). Likewise, we
observed an increase in NADPH oxidase activity and 3-nitrotyro-
sine-positive proteins in heart homogenates (Figure 4G, I).
Immunohistochemical analysis revealed that noise exposure
enhanced 3-nitrotyrosine staining throughout the vasculature (day 1–
4, Figure
5A), augmented 4-hydroxynonenal staining (day 1–4,
Supplementary material online, Figure 2S) and increased vascular ET-
1 levels on day 2, mainly within the endothelium (Figure
5B).
Effects of noise on gene expression in
MLEC
Noise exposure caused a significant increase in eNOS, HO-1, PGC-
1a and NOX-1 expression in freshly isolated mouse lung endothelial
cells (Supplementary material online, Figure 4S) from noise-exposed
animals. The changes in eNOS gene expression obtained in MLECsin
response to noise parallel changes in the aorta.
Figure 2 Effects of noise on vascular function, sensitivity to vasoconstrictors and vascular NO production. Relaxation by the endothelium-depend-
ent and -independent vasodilators acetylcholine (ACh, A) and nitroglycerin (NTG, B) were impaired by noise exposure. The sensitivity of the aorta
to vasoconstrictors like norepinephrine (C) and endothelin-1 (D) was increased upon noise exposure. Noise exposure for 1 and 4 days significantly
reduced the aortic NO production and bioavailability measured by EPR. (E) Quantification of the NO signal detected by Fe(DECT)
2
spin trapping. (F)
Representative NO traces of mice not exposed (Ctr.) and exposed to noise. For detailed statistical analysis see Supplementary material online, Tables
2S and 3S.Dataaremean±SDfromn =1326(A, B), 8–22 (C, D), 8–22 (E) mice/group.
Effects of noise on vascular function, oxidative stress, and inflammation 2841
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Effects of noise on invasion of the
vasculature with inflammatory cells
FACS analysis of mouse aorta revealed that noise exposure led to a
significant increase of myelomonocytic cells and natural killer cells
within the vasculature on day 1 or 4 (Supplementary material online,
Figure 5S, panels A, B). No significant increase in infiltration was
observed for neutrophils (Supplementary material online, Figure 5S,
panel C) and at least one significantly increased day for leucocytes in
general as well as macrophages and monocytes (Supplementary ma
terial online, Figure 5S, panel D). No significant changes were observed
for T cells (Supplementary material online, Figure 5S, panel D). The
gating strategy for FACS analysis is shown in Supplementary material
online, Figure 6S.
Effects of white noise on parameters of
vascular function and oxidative stress
Exposure of mice to white noise did not change ACh-dependent re-
laxation (Supplementary material online, Figure 7S). Also other par-
ameters of NO/cGMP signaling such as eNOS phosphorylation of
eNOS at Ser1177 and of VASP at Ser239, BH4 generating enzymes
GCH-1 and DHFR, sGC, cGK-1 showed no major changes in the
white noise group (Supplementary material online, Figure 7S and 8S).
Plasma 3-nitrotyrosine positive proteins and IL-6 were not changed
(Supplementary material online, Figure 7S). Aortic NADPH oxidase
subunits NOX-1 and NOX-2 were not up-regulated (Supplementary
material online,Figure7S) and endothelial superoxide formation was
not changed with no indication of eNOS uncoupling as determined
by L-NAME incubation (Supplementary material online,Figure9S)
and as supported by unaltered S-glutathionylation of eNOS
(Supplementary material online,Figure8S). Aortic ET-1 protein ex-
pression showed no major changes (Supplementary material online,
Figure 7S).
Next generation seque ncing
Comparative analysis of the transcriptomes of aortic tissue from noise
treated animals vs. controls showed numerous differentially expressed
genes. If a threshold of P < 0.05 and Log2 fold change >_0.5 is applied,
224 genes were categorized as transcriptionally either up- or down-
regulated over the entire experimental period. The majority of these
genes are down-regulated. Depending on the length of noise treat-
ment, the level of gene expression of individual genes can fluctuate
(see Supplementary material onlin e, Figure 10S). In Supplementary
material online, Figure 11S, highly differentially expressed gene prod-
ucts from the NGS data are presented in box plots over day 1, 2, and
4 of noise treatment. The four strongest up-regulated genes
compared with controls were Zbtb44, Setad4, Ypel2,andIhh. Similarly,
the amount of transcripts of Sacs, Nbeal1, PTPN4,andNR4A3 were sig-
nificantly reduced by noise. In Supplementary material online, Tables
4S and 5S, the 30 most highly up- and down-regulated genes are listed.
Pathway analysis by gene ontology annotation from NGS data
Figure 3 Effects of noise for 1, 2, and 4 days on endothelial NO-synthase protein expression and activity. (AC) Endothelial NO synthase protein
expression is increased after 4 days noise exposure and activating phosphorylation at Ser1177 is increased significantly at all time points measured.
(D) eNOS S-glutathionylation as a surrogate marker for uncoupling of the protein was increased significantly at all time points of noise exposure.
(E, F) Noise increased GTP-cyclohydrolase I (GCH-I) and dihydrofolate reductase (DHFR) expression leading to increased synthesis of the eNOS co-
factor tetrahydrobiopterin (BH
4
) responsible for the coupling of the enzyme. Data are mean ± SD from n = 6–8 samples (pooled from 2 to 3 mice
per sample) (A–C, E, F) and 7–10 samples (pooled from 2 mice per sample) (D).
2842 T. Mu¨nzel et al.
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Cites background from "Effects of noise on vascular functi..."

  • ...Importantly, these changes were unique for aircraft noise and not observed in response to white noise exposure (applied in the form of a continuous swoosh) (24), suggesting that the characteristics of the noise stimulus (pattern, frequency, exposure time, and intensity) are important....

    [...]

  • ...Nextgeneration sequencing analysis showed that aortic tissues from aircraft noise–treated animals displayed significant changes of genes partly responsible for the regulation of vascular function, vascular remodeling, and cell death (24)....

    [...]

  • ...Thus, noise-induced endothelial dysfunction may partly explain the association between transportation noise and CVD found in various epidemiological studies (24,25)....

    [...]

  • ...Our aim was to study the nonauditory effects of noise on the cardiovascular system, inflammation, and oxidative stress (24)....

    [...]

Journal ArticleDOI
Ning Xia1, Huige Li1
TL;DR: Repeated and chronic social stress leads to glucocorticoid resistance, enhanced myelopoiesis, upregulated proinflammatory gene expression, and oxidative stress, but the causal role of these mechanisms in the development of loneliness-associated CVD remains unclear.
Abstract: Significance: Social and demographic changes have led to an increased prevalence of loneliness and social isolation in modern society. Recent Advances: Population-based studies have demonstrated that both objective social isolation and the perception of social isolation (loneliness) are correlated with a higher risk of mortality and that both are clearly risk factors for cardiovascular disease (CVD). Lonely individuals have increased peripheral vascular resistance and elevated blood pressure. Socially isolated animals develop more atherosclerosis than those housed in groups. Critical Issues: Molecular mechanisms responsible for the increased cardiovascular risk are poorly understood. In recent reports, loneliness and social stress were associated with activation of the hypothalamic–pituitary–adrenocortical axis and the sympathetic nervous system. Repeated and chronic social stress leads to glucocorticoid resistance, enhanced myelopoiesis, upregulated proinflammatory gene expression, and oxidative...

219 citations

Journal ArticleDOI
TL;DR: Sies et al. as discussed by the authors defined a global concept of Oxidative Stress as an imbalance between oxidants and antioxidants in favor of the oxidants, leading to a disruption of redox signaling and control and/or molecular damage.

169 citations

References
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TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Abstract: Copyright (©) 1999–2012 R Foundation for Statistical Computing. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.

272,030 citations

Journal ArticleDOI
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Abstract: In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html .

47,038 citations

Journal ArticleDOI
TL;DR: G*Power 3 provides improved effect size calculators and graphic options, supports both distribution-based and design-based input modes, and offers all types of power analyses in which users might be interested.
Abstract: G*Power (Erdfelder, Faul, & Buchner, 1996) was designed as a general stand-alone power analysis program for statistical tests commonly used in social and behavioral research. G*Power 3 is a major extension of, and improvement over, the previous versions. It runs on widely used computer platforms (i.e., Windows XP, Windows Vista, and Mac OS X 10.4) and covers many different statistical tests of thet, F, and χ2 test families. In addition, it includes power analyses forz tests and some exact tests. G*Power 3 provides improved effect size calculators and graphic options, supports both distribution-based and design-based input modes, and offers all types of power analyses in which users might be interested. Like its predecessors, G*Power 3 is free.

40,195 citations

Journal ArticleDOI
TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
Abstract: Motivation Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. Results To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. Availability and implementation STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.

30,684 citations

Journal ArticleDOI
TL;DR: It is shown that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads, and estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired- end reads, depending on the number of possible splice forms for each gene.
Abstract: RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads. On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene. RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.

14,524 citations