Expression Analysis Of Asthma Candidate Genes During Human And Murine Lung Development
Little is known about the role of most asthma susceptibility genes during human lung development. Genetic determinants for normal lung development are not only important early in life, but also for later lung function. To investigate the role of expression patterns of well-defined asthma susceptibility genes during human and murine lung development. We hypothesized that genes influencing normal airways development would be over-represented by genes associated with asthma. Asthma genes were first identified via comprehensive search of the current literature. Next, we analyzed their expression patterns in the developing human lung during the pseudoglandular (gestational age, 7-16 weeks) and canalicular (17-26 weeks) stages of development, and in the complete developing lung time series of 3 mouse strains: A/J, SW, C57BL6. In total, 96 genes with association to asthma in at least two human populations were identified in the literature. Overall, there was no significant over-representation of the asthma genes among genes differentially expressed during lung development, although trends were seen in the human (Odds ratio, OR 1.22, confidence interval, CI 0.90-1.62) and C57BL6 mouse (OR 1.41, CI 0.92-2.11) data. However, differential expression of some asthma genes was consistent in both developing human and murine lung, e.g. NOD1, EDN1, CCL5, RORA and HLA-G. Among the asthma genes identified in genome wide association studies, ROBO1, RORA, HLA-DQB1, IL2RB and PDE10A were differentially expressed during human lung development. Our data provide insight about the role of asthma susceptibility genes during lung development and suggest common mechanisms underlying lung morphogenesis and pathogenesis of respiratory diseases.
RESEARC H Open Access
Expression analysis of asthma candidate genes
during human and murine lung development
, Alvin T Kho
, Sunita Sharma
, Roger Gaedigk
, J Steven Leeder
, Thomas J Mariani
Vincent J Carey
, Scott T Weiss
and Kelan G Tantisira
Background: Little is known about the role of most asthma susceptibility genes during human lung development.
Genetic determinants for normal lung development are not only important early in life, but also for later lung
Objective: To investigate the role of expression patterns of well-defined asthma susceptibility genes during human
and murine lung development. We hypothesized that genes influencing normal airways development would be
over-represented by genes associated with asthma.
Methods: Asthma genes were first identified via comprehensive search of the current literature. Next, we analyzed
their expression patterns in the developing human lung during the pseudoglandular (gestational age, 7-16 weeks)
and canalicular (17-26 weeks) stages of development, and in the complete developing lung time series of 3 mouse
strains: A/J, SW, C57BL6.
Results: In total, 96 genes with association to asthma in at least two human populations were identified in the
literature. Overall, there was no significant over-representation of the asthma genes among genes differentially
expressed during lung development, although trends were seen in the human (Odds ratio, OR 1.22, confidence
interval, CI 0.90-1.62) and C57BL6 mouse (OR 1.41, CI 0.9 2-2.11) data. However, differential expression of some
asthma genes was consistent in both developing human and murine lung, e.g. NOD1, EDN1, CCL5, RORA and HLA-
G. Among the asthma genes identified in genome wide association studies, ROBO1, RORA, HLA-DQB1, IL2RB and
PDE10A were differentia lly expressed during human lung development.
Conclusions: Our data provide insight about the role of asthma susceptibility genes during lung development and
suggest common mechanisms underlying lung morphogenesis and pathogenesis of respiratory disea ses.
Keywords: Asthma, Development, Expression, Genetics, Lung
There is good evidence that genetic factors strongly
influence the risk of asthma, and associations between
numerous genes and asthma have been evaluated in the
past decades [1,2]. Recent genome wide a ssociation
studies (GWAS) of asthma have identified several
additional asthma susceptibility genes [3-10]. Little is
genes during human lung development.
The “ development al origins” hypothesis  proposes
that specific in utero events at critical periods during
organogenesis and maturation result in long-term
physiological or metabolic changes, ultimately contribut-
ing to disease in later life [12,13]. Our group previously
showed that Wnt signal ing genes that were differentially
expressed during fetal lung development were associated
with impaired lung function in two cohorts of school-
aged asthmatic children . These results suggest the
importance of early life events in determining lung
function. They also highlight the benefit of integrating
gene expression and genetic association data to connect
transcriptomic events in the early developing lung to
genetic associations of lung function in later life.
* Correspondence: email@example.com
Channing Laboratory, Brigham and Women’s Hospital and Harvard Medical
School, Boston, MA, USA
Full list of author information is available at the end of the article
Melén et al. Respiratory Research 2011, 12:86
© 2011 Melén et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribu tion License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and repro duction in
any medium, provided the original work is properly cited.
Asthma is a disease characte rized by both airway
inflammation and smooth muscle contraction, leading
to airway obstruction. Dendritic cells, mast cells, and
T-lymphocytes, as well as airway smooth muscle cells,
all begin to appear within the lung parenchyma during
the pseudoglandular stage of lung development. We
therefore hypothesized that genes influencing normal
airways development, especially during the branching
morphogenesis stage of human lung development,
would be over-represented by genes associated with
asthma. To test this hypothe sis, we investigated the role
of a well-defined set of asthma susceptibility genes
during human and murine lung development. 96 asthma
genes were first identified via comprehensive search of
the current literature. Next, we analyzed their expres-
sion patterns in the developing human lung during the
pseudoglandular (gestational age, 7-16 weeks) and cana-
licular (1 7-27 weeks) stages of development, and in the
complete developing lung time series of 3 mouse strains:
A/J, SW and C57BL6.
We show that overall, there was no over-representa-
tion of the asthma genes among genes differentially
expressed during lung development, which may reflect
the diverse ontological contexts of the asthma genes.
However, some genes showed a consistent pattern of
differential expression in all developing lun g data sets,
e.g. NOD1, EDN1, RORA, CCL5 and HLA- G, which sug-
gests that these genes play a fundamental role in normal
The human fetal lung tissues were obtained from
National Institu te of Child Health and Human Develop-
ment supported tissue databases and microarray profiled
as previously described [14,15]. Creation of the tissue
repository was approved by the University of Missouri-
Kansas City Pediatric Institutional Review Board. 38
RNA samples from 38 subjects (estimated gestational
age 7-22 weeks or 53-154 days post conception) were
included in the analysis (Table 1). The murine data have
previously been described and their micr oarray data are
available at NCBI Gene Expression Omnibus (GEO,
http://www.ncbi.nlm.nih.gov/ge o); A/J , n = 24 sam-
ples; SW , n = 11; and C57BL6 mice , n = 5,
The developing human lung ti me series data is available
at NCBI Gene Expression Omnibus (GEO, http://www.
ncbi.nlm.nih.gov/geo), GSE14334 (Affymetrix Human
Genome GeneCh ip U133 Plus 2.0 microarray platform) .
Expression values were extracted and normalized from .
CEL files using the Affy package and the Robust
Multi-array Average (RMA) method in R/BioConductor
(http://www.bioconductor.org) which returns the mea-
sured expression signal of each micrroarray gene probe
in logarithmic base 2 scale. Validation of the human
microarray analysis by qPCR for gene s differentially
expressed during lung develo pment has been performed
earlier and this demonstrated that 83% of individual
gene expression trajectories could be replicated .
The developing whole mouse lung transcriptome data
from three different mouse strains were extracted and
normalized, separately, using RMA in R/BioConductor;
24 samples from A/J (Affymetrix Mu74Av2 platform);
11 samples from SW (Affymetrix Mu11K A and B plat-
forms); and 5 samples from C57BL6 (Affymetrix Mouse
430 Plus 2.0 platform).
A PubMed (http://www.ncbi.nlm.nih.gov/pubmed)
search was performed on March 8, 2010 using the
terms 1) “ asthma” together with 2) “genetic association”
or “ case control” in order to cover all published papers
between July 1, 2008 and December 31, 2009. We
applied the following inclusion criteria for an asthma
gene: 1) significant association with asthma affection
status in at least two populations and 2) at least one sig-
nificant association study with no fewer than 150 cases
Table 1 Summary characteristics of included human and murine lung data sets
Data sets Developmental period N
Human lungs 7-22 weeks prenatal 38 Affy U133 Plus
54,675 19,501 96 220 
Mouse A/J lungs 14 days prenatal - 4 weeks
24 Affy Mu74Av2 12,488 9,060 66 89 
Mouse SW lungs 12 days prenatal - 4 weeks
11 Affy Mu11K A
13,179 7,660 60 86 
11.5 days prenatal - 5 days
5 Affy Mouse 430
45,101 21,141 88 142 
* CCL26, GSDMB, HLA-DQB1, PTPRD, TLR10 and WDR36 do not have a mouse orthologue gene.
Melén et al. Respiratory Research 2011, 12:86
Page 2 of 10
and 150 controls or 150 trios. Genes identified through
three earlier literature searches based on papers pub-
lished before July 1, 2008 were also included if they met
our two predefined criteria [1,19,20]. In addition, all
GWAS of asthma published through September 2010,
were also evaluated and asthma genes were i ncluded if
our criteria were met. Please see Supplemental data for
details about the asthma genes included in our analyses.
Mouse orthologues of human genes were identified
using NCBI’s HomoloGene database (http://www.ncbi.
Differential gene expression analysis relative to gesta-
tional age was performed using a linear regression
model (lmFit) as implemented in the Limma package in
R/BioConductor. Each microarray gene probe’s logarith-
mic base 2 expression signal was regressed against the
gestational age as a continuous v ariable representing
days of the developing lung. We adjusted f or multiple
testing using the Benjamini and Hochberg method,
which controls the false discovery rate (i.e. the ex pected
proportion of false discoveries amongst the rejected
hypotheses), and the adjusted p-values were used to
declare a significant gene expression pattern over age
. “Differentially expressed” refers to an adjusted p-
value of <0.05 in the linear regression model. Fisher’s
exact test was next performed in Stata Statistical Soft-
ware (Collage Station, Tx) to test whether microrarray
probes representing predefined asthma genes were ove r-
represented among differentially expressed probes rela-
tive to probes representing “non-asthma genes” .This
analysis was restricted to microarray probes that were
gene annotated because the asthma gene probes were all
annotated. The same analysis steps were performed i n
human and murine data sets. Gene ontology (GO)
enrichment analysis was performed using DAVID (The
Database for Annotation, Visualization and Integrate d
In total, 96 asthma susceptibility genes were identified in
the literature (Additional file 1, Table E1 [1,3-10,24-96]).
All genes show significant associa tion with asthma in at
least two human populations, one of which has no fewer
than 150 cases and 150 controls or 150 trios. The 96
genes were represented by 220 probes on the human
microarray (Table 1). Not all human genes have a
mouse orthologue and the mouse microarray data sets
have slightly lower numbers of asthma genes and their
corresponding microarray probes.
We found that 28% of all microarray probes in the
human data set were differentially expressed during the
analyzed lung development period (human estimated
gestational age 7-22 weeks), Table 2. A similar figure
was seen in the A/J mouse and somewhat lower figures
in the SW and C57BL6 mouse strains. Gene ontol ogy
(GO) enrichment analysis using DAVID of the human
list of differentially expressed genes returned 879 signifi-
cant GO terms, of which 6 terms pertain directly to th e
lung development. Among the asthma gene prob es, 32%
were differentially expressed during early human lung
development. While there was a trend towards over-
representation (Odds ratio, OR 1.22, CI 0.90-1.62) this
was not statistically significant in comparison to the
non-asthma gene probes (28%). In agreement with the
human data, no over-representation of asthma gene
probes was found among probes differentially expres sed
during lung development in mice strains, although there
was a trend in the C57BL6 strain (OR 1.41, CI 0.92-
2.11), Table 2.
Although asthma genes as a group was not differen-
tially expressed more than non-asthma genes during
early lung development, some genes were consistently
Table 2 Proportion of the asthma gene probes among probes differentially expressed during lung development in
human and mouse data sets
Human lungs Mouse A/J lungs Mouse SW lungs Mouse C57BL6 lungs
Asthma probes Asthma probes Asthma probes Asthma probes
Differentially expressed Yes No Total* Yes No Total* Yes No Total* Yes No Total*
Yes 71 11373 11444 25 3285 3310 15 2052 2067 32 6637 6669
No 149 29017 29166 64 8511 8575 71 9189 9260 110 32161 32271
Total 220 40390 40610 89 11796 11885 86 11241 11327 142 38798 38940
% differentially expressed probes 32 28 28 28 28 28 17 18 18 23 17 17
p-value† 0.18 1.0 1.0 0.09
OR (95% CI) 1.22 (0.90-1.63) 1.01 (0.61-1.63) 0.95 (0.50-1.67) 1.41 (0.92-2.11)
* Analyses restricted to probes represented by annotated genes.
† Fisher’s exact test.
“Differentially expressed” refers to an adjusted p-value of <0.05 in the linear regression model.
OR = Odds ratio. CI = Confidence interval.
Melén et al. Respiratory Research 2011, 12:86
Page 3 of 10
different ial expressed, as listed in Table 3 (see full list in
Additional file 1, Table E2). Expression of NOD1, E DN1
and IL4R were positively correlated with gestational age
in the human data, whereas ROBO1 and PLAUR were
negatively correlated (i.e. lower expression levels the
higher gestational age). Among the asthma genes identi-
fied in GWAS, ROBO1, RORA, HLA-DQB1, IL2RB and
PDE10A showed most significantevidenceofinvolve-
ment in lung development (all adjusted p < 0.001 for
differential e xpression). Analyses were also done com-
paring gene expression patte rns between the pseudo-
glandular (primary branching morphogenesis stage) and
canalicular stages (with 112 days post conception as the
dividing time point between the 2 stages). The list of
top genes differentially expressed between these two
stages (Additional file 1, Table E3 and Figure E1) corre-
sponds well with the list of top genes using time as a
continuous variable (Table 3).
Next, we evaluated all differentially expressed asthma
gene s in the human data set to see which genes showed
a consistent expression pattern across human and mur-
ine data sets. Table 4 shows all genes with at least one
significant probe per gene in the human data and at
with adjusted p-value <0.05). Eight genes had one or
more significant probes in all dat a sets, with NOD1,
EDN1, CCL5, RORA and HLA-G showing the most con-
sistent expression patterns across human and mouse
(see detailed EDN1/Edn1 expression over time in
human and mouse lung tissue; Figure 1 and 2). In terms
of bio-ontolo gic enrichment, the 19 asthma genes con-
sistently differentially expressed in human and mouse
lung development were enriched for ontological attri-
butes “ Regulation of cytokine production” (IRAK3,
CD86 , NOD1, TNF, IL18, SCGB1A1)and“Regulation of
cell activation” (STAT6, CD86, IL18, IL 4R, RORA,
SCGB1A1) (Additional file 1, Table E4.) In terms of
gene product characteristics, “ Disulfide bond” ,
“ Se creted” and “ Signal peptide” are attributes of a
majority of the genes. 15 of the 19 genes in Table 4
have been extensively studied in human and murine
experiments that s upport their involvement in asthma
pathogenesis (Additional file 1, Table E5).
In orde r to disentangle pre- and postnatal expression
patterns in the murine data sets, separate pre- and post-
natal analyses were a ttempted. However, this subgroup
analysis was not meaningful for the SW and C56BL6
data sets because of substantially reduced sample size.
The A/J data contains two prenatal time points (day 11
shows overlapping results for human and prenatal A/J
data. Eight of the previously identified 19 genes with
consistent expression pattern across human and murine
data sets (Table 4) were also identified when prenatal
A/J data was used (including Edn1).
Little is known about the role of most asthma suscept-
ibility genes during human lung development. Here we
present a thorough evaluation of gene expression
patterns of current published asthma genes in the devel-
oping human and murine lung. While there was no gen-
eral over-representation of asthma genes among
differentially expressed genes, some asthma genes were
consistently differentia lly expressed in mu ltiple develop-
inglungtranscriptomes,e.g.NO D1, EDN1, CCL5,
RORA and HLA-G suggesting key functional roles in
Determinants for a normal lung development are criti-
cal not only early in life, but also for later lung function.
Longitudinal studies have shown that infants wit h
reduced lung function have an increased risk of develop-
ing asthma and respiratory illness later in life [97,98].
Shared genetic factors for reduced lung function in chil-
dren with asthma and adults who smoke (e.g. MMP12
variants) emphasize t he role of genetics on long term
lung function . Wnt signaling genes (e.g. Wif1,
Wisp1) were not identified as asthma genes in our
literature search, and were thus not included in our ana-
lyses. In our previous article by Sharma et al, Wif1 and
Wisp1 were differentially expressed during fetal lung
development and polymorphisms in these genes also
Table 3 Gene expression analysis of specific asthma
genes and evidence for differential expression during
human lung development (adjusted p < 0.001 cut off)
Probe id Average
NOD1 221073_s_at 7.6 7.0E-8 0.012
EDN1 222802_at 9.3 1.6E-6 0.026
EDN1 218995_s_at 8.6 4.4E-6 0.019
ROBO1 213194_at 10.2 1.5E-5 -0.009
IL4R 203233_at 7.3 3.3E-5 0.010
RORA 226682_at 8.2 3.5E-5 0.022
RORA 236266_at 5.2 5.2E-5 0.011
HPCAL1 212552_at 9.4 5.4E-5 0.012
212998_x_at 4.8 1.5E-4 0.012
PLAUR 210845_s_at 5.9 2.0E-4 -0.008
IL2RB 205291_at 6.5 2.5E-4 0.007
CCL5 204655_at 4.7 2.6E-4 0.008
HPCAL1 205462_s_at 7.3 4.6E-4 0.013
TLR10 223751_x_at 4.1 4.9E-4 0.005
PDE10A 205501_at 6.4 6.3E-4 -0.011
CCL5 1405_i_at 4.1 9.9E-4 0.008
* Adjusted p-value (B-H method) for differential expression over time.
† The beta coefficient corresponds to the mean change in gene expression
per day during the studied period (7-22 weeks of gestational age).
Melén et al. Respiratory Research 2011, 12:86
Page 4 of 10
Table 4 Genes with at least one significant probe per gene in the human data and at least in one mouse data set
(adjusted p-value <0.05)
NOD1 Nod1 0.012 --0.133 7.0E-8 --2.1E-2 4.7E-9
EDN1 Edn1 0.026 0.018 0.054 0.138 1.6E-6 7.4E-3 1.4E-3 2.4E-2 3.9E-11
ROBO1 Robo1 -0.009 -0.014 - -0.055 1.5E-5 3.8E-2 - 9.4E-2 6.9E-7
IL4R Il4ra 0.01 0.033 0.032 0.1 3.4E-5 3.0E-5 2.3E-2 5.5E-2 5.8E-11
RORA Rora 0.022 0.01 0.025 0.107 3.5E-5 1.3E-2 9.2E-3 2.1E-2 5.5E-9
PLAUR Plaur -0.008 0.013 0.015 0.106 2.0E-4 2.3E-2 5.2E-2 2.1E-2 9.8E-1
CCL5 Ccl5 0.008 0.022 0.027 0.079 2.6E-4 1.6E-7 1.9E-3 2.0E-2 5.5E-13
IRAK3 Irak3 -0.011 --0.073 1.3E-3 --4.5E-2 2.0E-2
IL18 Il18 0.004 0.01 0.018 0.139 1.6E-3 4.4E-4 2.4E-2 2.7E-1 1.3E-7
STAT6 Stat6 0.007 0.021 0.002 0.106 1.8E-3 1.6E-2 6.0E-1 4.7E-2 2.5E-5
CHIA Chia 0.009 0.077 0.039 0.288 1.8E-3 5.7E-3 3.4E-1 3.3E-2 4.0E-6
HLA-G H2-M3 0.01 0.021 0.032 0.103 2.6E-3 2.9E-5 9.2E-4 1.7E-2 3.7E-10
CD86 Cd86 0.003 0.001 0.008 0.097 5.6E-3 9.3E-1 1.3E-1 3.1E-2 1.9E-3
PRNP Prnp -0.003 0.02 0.031 0.106 8.9E-3 8.8E-3 1.1E-1 7.2E-2 5.0E-1
PCDH1 Pcdh1 0.006 --0.232 1.0E-2 --3.1E-2 1.6E-3
SERPINE1 Serpine1 0.021 0.018 0.02 0.129 1.6E-2 4.5E-5 9.6E-3 1.7E-2 3.3E-8
TNF Tnf 0.004 -0.003 0.007 0.051 2.3E-2 3.7E-1 2.6E-1 4.9E-2 4.5E-2
TLE4 Tle4 -0.004 -0.009 0.006 -0.07 2.3E-2 1.0E-3 3.1E-1 3.0E-1 1.0E-3
SCGB1A1 Scgb1a1 0.017 0.163 0.09 0.736 3.8E-2 1.2E-3 5.1E-2 1.8E-2 4.6E-6
* The beta coefficient corresponds to the mean change in gene expression per day during the studied period.
† Adjusted p-value (B-H method). ‡ Combined p-value for all data sets (human and murine) using the weighted z-score method.
Empty boxes (-) indicate that the gene was not represented on the chip. Bolded rows indicate genes with at least one significant probe per gene in all tested
data sets (adjusted p-value <0.0 5).
Figure 1 Expression of EDN1 over time in human lung tissue in
relation to time (days post conception), p = 1.6E-6 for
differential expression. The fitted line through the data represents
the beta coefficient from linear regression analysis.
Figure 2 Expression of Edn1 over t ime in mouse whole l ung
tissue in relation to time (days post conception). Solid circles
represent the A/J data (p = 0.007 for differential expression), open
squares represent the C57BL6 data (p = 0.02) and solid triangles
represent the SW data (p = 0.001). The fitted line through each data
set represents the beta coefficient from linear regression analysis.
Melén et al. Respiratory Research 2011, 12:86
Page 5 of 10
showed association with lun g function measured as
FEV1 and FVC, but association to asthma per se was
not tested .
The transcriptional control of lung morphogenesis is
key for normal development f rom primordium to a
fully differentiated, functioning organ [100,101].
Human lung growth has historically been categorised
into five stages based on histological and anatomical
characteristics: embryonic (26 days to 5 weeks), pseu-
doglandular (5-16 weeks), canalicular (16-26 weeks),
saccular (26 weeks to birth), an d alveolar (birth to 6
months) . Additional “ molecular” phases wit hin
the pseudoglandular stage have been observed, which
extends our knowledge of lung development beyond
traditional embryology .
GWAS have co ntributed to important knowledge
about underlying functional genetics i n many complex
diseases . The majority of trait associated SNPs
show weak to moderate effect sizes, which supports ear-
lier evidence that complex diseases result from several
genetic and, often, environmental factors. Evid ence of a
functional role is also lacking for most identified genes.
In order to increase our understanding of the mechan-
ism and potential function of asthma susceptibility
genes identified in published GWAS and “ classic”
asthma candidate gen es, we evaluated their gene expres-
sion patterns in the developing human lung. Compara-
tive analyses also showed that many of the differential ly
expressed genes in the human data set were also differ-
entially expressed during murine lung development.
Among the GWAS asthma genes, ROBO1, RORA, HLA-
DQB1, IL2RB and PDE10A were differentially expressed
in the human data. These genes represent a wide range
of structural and ontological families with different
assumed functions, but their potential involvement in
lung development has previously not been thoroughly
evaluated. Regulation of cytokine production and cell
activation were the most significant bio-ontologic attri-
butes to genes differentialy expressed during lung
Using the murine data sets for comparative analyses,
RORA, which encodes for a nuclear hormone receptor,
showed the most consistent expression pattern (expres-
sion positively correlated with gestational age in all data
sets). ROBO1 expression was on the other hand nega-
tively correlated with gestational age in all tested data
sets (albeit significant in only 2/3 sets), which indic ates
an important effect early in the developing lung and
then a diminishing effect over time. The ROBO1 protein
is involved in axon guidance and neuronal precursor cell
migration. PTGDR, WDR36, PRNP, DENND1B, PDE4D,
TLE4 and TSLP also showed weak evidence of differen-
tial expression in the human data using adjusted p <
0.05 as cut off (Additional file 1, Table E2), but none
showed consistent gene expression patterns in the mur-
ine data sets.
NOD1 showed the strongest evidence for differential
expression in the human data and this pattern was con-
sistent in the C57BL6 strain. However, Nod1 was not
represented on the platforms used for analyses on the
A/J and SW strains and could thus not b e evaluated in
these data sets (also true for another asthma gene with
consistent expression patterns, PCDH1 ). NOD1
encodes for a cytosolic protein which contains an N-
term inal caspase recruitment domain (CARD) and plays
an important role for recognition of bacterial com-
pounds and initiation of the innate immune response
. Little i s known about the role of NOD1 during
lung development and our findings indicate that NOD1
could have important contribution.
EDN1 was the second most differentially expressed
asthma gene in the human data set and very consistent
expression patterns were found in all murine data sets.
Also for the embryonic stage analyses (pseudoglandular
vs canalicular), EDN1 was among the most highly differ-
entially expressed genes. In general, embryonic stage
results were very similar to the results using time as a
continuous variable. EDN1 belong to a family of
secreted peptides pro duced by vascular endothelial cells
with multiple effects on cardiovascular, neural, pulmon-
ary and renal physiology [104,105]. EDN1 shows invol-
vement in pulmonary hypertension, fibrosis, obstr uctive
diseases and acute lung injury, a nd is also required for
the normal development of several tissues. Mice lacking
the Edn1 gene die of respiratory failure at birth and
show severe craniofacial abnormalities, as well as cardio-
vascular defects [106,1 07]. Transgenic m ice with lung-
specific over-expression of the human EDN1 gene
develop, on the other hand, chronic lung inflammati on
and fibrosis . Edn1 heterozygous knockout mice
also show increased bronchial responsiveness and these
result link EDN1 functionally to asthma and obstructive
diseases . To date, three studies report significant
association between EDN1 and asthma [41,109,110].
Our data, as well as previous studies, point to an impor-
tant role for EDN1 in normal lung development, which
warrants further studies.
Our study has several limitations. Our 38 human lung
tissue samples were restricted to the pseudo glandular
and canalicular stages. Information about key exposures
that could influence gene expression patterns, such as
maternal smoking, residential area, and parental allergy
is not available. Thirty-eight samples are a relatively
small sample size for expression analys es due to human
biological variation and fe tal lung tissue during the later
stages of gestation was not available. It is possible that
some asthma genes are important for human lung devel-
opment during the later stages of gestation, but we were
Melén et al. Respiratory Research 2011, 12:86
Page 6 of 10
complement the human data, we analysed expression
patterns from early gestational to postnatal stages of
lung development in three different murine strains. We
used this murine data to replicate, in silico, the human
results in the early stages and to infer human gene
expression pattern in the later stages of the developing
lung. Also, the m icroarray platforms used in the
included data sets do not entirely co ver the human (and
murine) t ranscriptome and important genes may have
been missed (e.g. GPRA/NPSR1  is not represented
on the U133 Plus 2.0 microarray chip and could not be
evaluated). Protein analyses could provide a better view
to understand specific gene functions and the post-tran-
scriptional regulation level, but such data was not avail-
able in our study. Our asthma gene list represents genes
that met our predefined criteria for asthma association,
and some genes genes may have been missed (e.g. those
only captured by the search terms “ family based study”
AND “ asthma” ). Given the rapid rate at whi ch novel
asthma susceptibility loci are being discovered, some of
the most recent asthma genes may have been missed.
These may introduce a potential null bias in the
We have evaluated gene expression p atterns of asthma
susceptibility genes identified via a comprehensive litera-
ture search of candidate gene studies and GWAS pub-
lished to date. We found strong and consistent evidence of
differential expression of several asthma genes in the
developing human and murine lung. Among genes identi-
fied in asthma GWAS, ROBO1, RORA, HLA-DQB1, IL2RB
and PDE10A showed most consistent expression patterns
and from asthma candidate genes, e.g. NOD1, EDN1,
CCL5 and HLA-G were identified. Our analyses prov ide
functional insight about asthma susceptibility genes during
normal lung development, which improves our under-
standing about normal and pathological processes related
to respiratory diseases in children and adults.
Additional file 1: Supplementary Tables and Figure. Expression
analysis of asthma candidate genes during human and murine lung
List of abbreviations
CI: Confidence interval; DAVID: Database for Annotation, Visualization and
Integrated Discovery; GEO: Gene Expression Omnibus; GO: Gene ontology;
GWAS: Genome wide association studies; NCBI: National Center for
Biotechnology Information; OR: Odds ratio; qPCR: Quantitative real time
polymerase chain reaction.
The authors wish to thank Dr. Weiliang Qiu, Channing Laboratory, Brigham
and Women’s Hospital and Harvard Medical School, for a valuable statistical
review. Financial support: Supported by National Institutes of Health grants
K25 HL91124, R01 HL88028, and P50 NS40828 (ATK.); R01 ES10855 (JSL); R01
HL097144 (STW), U01 HL65899 (STW and KGT); EM is supported by post doc
grants from the Swedish Heart Lung Foundation, the Swedish Fulbright
Commission, Centre for Allergy Research, Karolinska Institutet and
Riksbankens Jubileumsfond, Erik Rönnberg’s scholarship for research on early
Channing Laboratory, Brigham and Women’s Hospital and Harvard Medical
School, Boston, MA, USA.
Institute of Environmental Medicine, Karolinska
Institutet, Stockholm, Sweden.
Astrid Lindgren Children’s Hospital, Karolinska
University Hospital, Stockholm, Sweden.
Children’s Hospital Informatics
Program, Boston, MA, USA.
Division of Pulmonary and Critical Care
Medicine, Brigham and Women’s Hospital, Boston, MA, USA.
Clinical Pharmacology and Medical Toxicology, Department of Pediatrics,
Children’s Mercy Hospitals and Clinics, Kansas City, MO, USA.
Neonatology and Center for Pediatric Biomedical Research, University of
Rochester, Rochester NY, USA.
Partners Center for Personalized Genetic
Medicine, Boston, MA, USA.
EM carried out the literature search and the statistical analyses together with
ATK, SS and VJC. EM, RG, JSL, TJM, STW and KGT participated in the design
and planning of the study. EM, ATK and KGT drafted the manuscript. All
authors read and approved the final manuscript.
All authors declare no competing interests and no support from any
organisation for the submitted work; no financial relationships with any
organisations that might have an interest in the submitted work in the
previous 3 years; no other relationships or activities that could appear to
have influenced the submitted work.
Received: 15 March 2011 Accepted: 23 June 2011
Published: 23 June 2011
1. Ober C, Hoffjan S: Asthma genetics 2006: the long and winding road to
gene discovery. Genes Immun 2006, 7(2):95-100.
2. Rogers AJ, Raby BA, Lasky-Su JA, Murphy A, Lazarus R, Klanderman BJ,
Sylvia JS, Ziniti JP, Lange C, Celedon JC, Silverman EK, Weiss ST: Assessing
the reproducibility of asthma candidate gene associations, using
genome-wide data. Am J Respir Crit Care Med 2009, 179(12):1084-1090.
3. Gudbjartsson DF, Bjornsdottir US, Halapi E, Helgadottir A, Sulem P,
Jonsdottir GM, Thorleifsson G, Helgadottir H, Steinthorsdottir V,
Stefansson H, Williams C, Hui J, Beilby J, Warrington NM, James A,
Palmer LJ, Koppelman GH, Heinzmann A, Krueger M, Boezen HM,
Wheatley A, Altmuller J, Shin HD, Uh ST, Cheong HS, Jonsdottir B,
Gislason D, Park CS, Rasmussen LM, Porsbjerg C, et al: Sequence variants
affecting eosinophil numbers associate with asthma and myocardial
infarction. Nat Genet 2009, 41(3):342-347.
4. Hancock DB, Romieu I, Shi M, Sienra-Monge JJ, Wu H, Chiu GY, Li H, del
Rio-Navarro BE, Willis-Owens SA, Weiss ST, Raby BA, Gao H, Eng C,
Chapela R, Burchard EG, Tang H, Sullivan PF, London SJ: Genome-wide
association study implicates chromosome 9q21.31 as a susceptibility
locus for asthma in mexican children. PLoS Genet 2009, 5(8):e1000623.
5. Himes BE, Hunninghake GM, Baurley JW, Rafaels NM, Sleiman P,
Strachan DP, Wilk JB, Willis-Owen SA, Klanderman B, Lasky-Su J, Lazarus R,
Murphy AJ, Soto-Quiros ME, Avila L, Beaty T, Mathias RA, Ruczinski I,
Barnes KC, Celedon JC, Cookson WO, Gauderman WJ, Gilliland FD,
Hakonarson H, Lange C, Moffatt MF, O’Connor GT, Raby BA, Silverman EK,
Weiss ST: Genome-wide association analysis identifies PDE4D as an
asthma-susceptibility gene. Am J Hum Genet 2009, 84(5):581-593.
6. Li X, Howard TD, Zheng SL, Haselkorn T, Peters SP, Meyers DA, Bleecker ER:
Genome-wide association study of asthma identifies RAD50-IL13 and
HLA-DR/DQ regions. J Allergy Clin Immunol 2010, 125(2):328-335, e311.
Melén et al. Respiratory Research 2011, 12:86
Page 7 of 10
7. Mathias RA, Grant AV, Rafaels N, Hand T, Gao L, Vergara C, Tsai YJ, Yang M,
Campbell M, Foster C, Gao P, Togias A, Hansel NN, Diette G, Adkinson NF,
Liu MC, Faruque M, Dunston GM, Watson HR, Bracken MB, Hoh J, Maul P,
Maul T, Jedlicka AE, Murray T, Hetmanski JB, Ashworth R, Ongaco CM,
Hetrick KN, Doheny KF, et al: A genome-wide association study on
African-ancestry populations for asthma. J Allergy Clin Immunol 2009.
8. Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, von
Mutius E, Farrall M, Lathrop M, Cookson WO, consortium G: A large-scale,
consortium-based genomewide association study of asthma. N Engl J
Med 2010, 363(13):1211-1221.
9. Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, Heath S, Depner M,
von Berg A, Bufe A, Rietschel E, Heinzmann A, Simma B, Frischer T, Willis-
Owen SA, Wong KC, Illig T, Vogelberg C, Weiland SK, von Mutius E,
Abecasis GR, Farrall M, Gut IG, Lathrop GM, Cookson WO: Genetic variants
regulating ORMDL3 expression contribute to the risk of childhood
asthma. Nature 2007, 448(7152) :470-473.
10. Sleiman PM, Flory J, Imielinski M, Bradfield JP, Annaiah K, Willis-Owen SA,
Wang K, Rafaels NM, Michel S, Bonnelykke K, Zhang H, Kim CE,
Frackelton EC, Glessner JT, Hou C, Otieno FG, Santa E, Thomas K, Smith RM,
Glaberson WR, Garris M, Chiavacci RM, Beaty TH, Ruczinski I, Orange JM,
Allen J, Spergel JM, Grundmeier R, Mathias RA, Christie JD, et al: Variants of
DENND1B associated with asthma in children. N Engl J Med 2010,
11. Barker DJ, Martyn CN: The maternal and fetal origins of cardiovascular
disease. J Epidemiol Community Health 1992, 46(1):8-11.
12. Barker DJ: In utero programming of chronic disease. Clin Sci (Lond) 1998,
13. Stick S: Pediatric origins of adult lung disease. 1. The contribution of
airway development to paediatric and adult lung disease. Thorax 2000,
14. Sharma S, Tantisira K, Carey V, Murphy AJ, Lasky-Su J, Celedon JC, Lazarus R,
Klanderman B, Rogers A, Soto-Quiros M, Avila L, Mariani T, Gaedigk R,
Leeder S, Torday J, Warburton D, Raby B, Weiss ST: A Role for WNT-
Signaling Genes in the Pathogenesis of Impaired Lung Function in
Asthma. Am J Respir Crit Care Med 2009.
15. Kho AT, Bhattacharya S, Tantisira KG, Carey VJ, Gaedigk R, Leeder JS,
Kohane IS, Weiss ST, Mariani TJ: Transcriptomic analysis of human lung
development. Am J Respir Crit Care Med 2009, 181(1):54-63.
16. Bonner AE, Lemon WJ, You M: Gene expression signatures identify novel
regulatory pathways during murine lung development: implications for
lung tumorigenesis. J Med Genet 2003, 40(6):408-417.
17. Mariani TJ, Reed JJ, Shapiro SD: Expression profiling of the developing
mouse lung: insights into the establishment of the extracellular matrix.
Am J Respir Cell Mol Biol 2002, 26(5):541-548.
18. Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS:
Analysis of gene expression in a developmental context emphasizes
distinct biological leitmotifs in human cancers. Genome Biol 2008, 9(7):
19. Weiss ST, Raby BA, Rogers A: Asthma genetics and genomics 2009. Curr
Opin Genet Dev 2009, 19(3):279-282.
20. Vercelli D: Discovering susceptibility genes for asthma and allergy.
Rev Immunol 2008, 8(3):169-182.
21. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical
and powerful approach to multiple testing. J R Stat Soc B 1995,
22. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA:
DAVID: Database for Annotation, Visualization, and Integrated Discovery.
Genome Biol 2003, 4(5) :P3.
23. Huang da W, Sherman BT, Lempicki RA: Systematic and integrative
analysis of large gene lists using DAVID bioinformatics resources. Nat
Protoc 2009, 4(1):44-57.
24. Bailey MT, Kierstein S, Sharma S, Spaits M, Kinsey SG, Tliba O, Amrani Y,
Sheridan JF, Panettieri RA, Haczku A: Social stress enhances allergen-
induced airway inflammation in mice and inhibits corticosteroid
responsiveness of cytokine production. J Immunol 2009,
25. Barton SJ, Koppelman GH, Vonk JM, Browning CA, Nolte IM, Stewart CE,
Bainbridge S, Mutch S, Rose-Zerilli MJ, Postma DS, Maniatis N, Henry AP,
Hall IP, Holgate ST, Tighe P, Holloway JW, Sayers I: PLAUR polymorphisms
are associated with asthma, PLAUR levels, and lung function decline. J
Allergy Clin Immunol 2009, 123(6):1391-1400, e1317.
26. Batra J, Pratap Singh T, Mabalirajan U, Sinha A, Prasad R, Ghosh B:
Association of inducible nitric oxide synthase with asthma severity, total
serum immunoglobulin E and blood eosinophil levels. Thorax 2007,
27. Berlin AA, Lincoln P, Tomkinson A, Lukacs NW: Inhibition of stem cell
factor reduces pulmonary cytokine levels during allergic airway
responses. Clin Exp Immunol 2004, 136(1):15-20.
28. Berry MA, Hargadon B, Shelley M, Parker D, Shaw DE, Green RH,
Bradding P, Brightling CE, Wardlaw AJ, Pavord ID: Evidence of a role of
tumor necrosis factor alpha in refractory asthma. N Engl J Med 2006,
29. Bierbaum S, Nickel R, Koch A, Lau S, Deichmann KA, Wahn U, Superti-
Furga A, Heinzmann A: Polymorphisms and haplotypes of acid
mammalian chitinase are associated with bronchial asthma. Am J Respir
Crit Care Med 2005, 172(12):1505-1509.
30. Bosse Y, Lemire M, Poon AH, Daley D, He JQ, Sandford A, White JH,
James AL, Musk AW, Palmer LJ, Raby BA, Weiss ST, Kozyrskyj AL, Becker A,
Hudson TJ, Laprise C: Asthma and genes encoding components of the
vitamin D pathway. Respir Res 2009, 10:98.
31. Buckova D, Izakovicova Holla L, Vacha J: Polymorphism 4G/5G in the
plasminogen activator inhibitor-1 (PAI-1) gene is associated with IgE-
mediated allergic diseases and asthma in the Czech population. Allergy
32. Cameron L, Depner M, Kormann M, Klopp N, Illig T, von Mutius E,
Kabesch M: Genetic variation in CRTh2 influences development of
allergic phenotypes. Allergy 2009, 64(10):1478-1485.
33. Castro-Giner F, Kunzli N, Jacquemin B, Forsberg B, de Cid R, Sunyer J,
Jarvis D, Briggs D, Vienneau D, Norback D, Gonzalez JR, Guerra S, Janson C,
Anto JM, Wjst M, Heinrich J, Estivill X, Kogevinas M: Traffic-related air
pollution, oxidative stress genes, and asthma (ECHRS). Environ Health
Perspect 2009, 117(12):1919-1924.
34. Chatila TA: Interleukin-4 receptor signaling pathways in asthma
pathogenesis. Trends Mol Med 2004, 10(10):493-499.
35. Chatterjee R, Batra J, Das S, Sharma SK, Ghosh B: Genetic association of
acidic mammalian chitinase with atopic asthma and serum total IgE
levels. J Allergy Clin Immunol 2008, 122(1):202-208, 208 e201-207.
36. Chelbi H, Ghadiri A, Lacheb J, Ghandil P, Hamzaoui K, Hamzaoui A,
Combadiere C: A polymorphism in the CCL2 chemokine gene is
associated with asthma risk: a case-control and a family study in Tunisia.
Genes Immun 2008, 9(7):575-581.
37. Chen YQ, Shi HZ: CD28/CTLA-4–CD80/CD86 and ICOS–B7RP-1
costimulatory pathway in bronchial asthma. Allergy 2006, 61(1):15-26.
38. Cho SH, Hall IP, Wheatley A, Dewar J, Abraha D, Del Mundo J, Lee H,
Oh CK: Possible role of the 4G/5G polymorphism of the plasminogen
activator inhibitor 1 gene in the development of asthma. J Allergy Clin
Immunol 2001, 108(2):212-214.
39. Chu EK, Cheng J, Foley JS, Mecham BH, Owen CA, Haley KJ, Mariani TJ,
Kohane IS, Tschumperlin DJ, Drazen JM: Induction of the plasminogen
activator system by mechanical stimulation of human bronchial
epithelial cells. Am J Respir Cell Mol Biol 2006, 35(6):628-638.
40. Crosby JR, Guha M, Tung D, Miller DA, Bender B, Condon TP, York-
DeFalco C, Geary RS, Monia BP, Karras JG, Gregory SA: Inhaled CD86
antisense oligonucleotide suppresses pulmonary inflammation and
airway hyper-responsiveness in allergic mice. J Pharmacol Exp Ther 2007,
41. Daley D, Lemire M, Akhabir L, Chan-Yeung M, He JQ, McDonald T,
Sandford A, Stefanowicz D, Tripp B, Zamar D, Bosse Y, Ferretti V,
Montpetit A, Tessier MC, Becker A, Kozyrskyj AL, Beilby J, McCaskie PA,
Musk B, Warrington N, James A, Laprise C, Palmer LJ, Pare PD, Hudson TJ:
Analyses of associations with asthma in four asthma population samples
from Canada and Australia. Hum Genet 2009, 125(4):445-459.
42. Goenka S, Kaplan MH: Transcriptional regulation by STAT6. Immunol Res
43. Hattori T, Konno S, Hizawa N, Isada A, Takahashi A, Shimizu K, Gao P,
Beaty TH, Barnes KC, Huang SK, Nishimura M: Genetic variants in the
mannose receptor gene (MRC1) are associated with asthma in two
independent populations. Immunogenetics 2009, 61(11-12):731-738.
44. Higa S, Hirano T, Mayumi M, Hiraoka M, Ohshima Y, Nambu M,
Yamaguchi E, Hizawa N, Kondo N, Matsui E, Katada Y, Miyatake A, Kawase I,
Tanaka T: Association between interleukin-18 gene polymorphism 105A/
C and asthma. Clin Exp Allergy 2003, 33(8):1097-1102.
Melén et al. Respiratory Research 2011, 12:86
Page 8 of 10
45. Hong X, Zhou H, Tsai HJ, Wang X, Liu X, Wang B, Xu X, Xu X: Cysteinyl
leukotriene receptor 1 gene variation and risk of asthma. Eur Respir J
46. Hossny EM, Amr NH, Elsayed SB, Nasr RA, Ibraheim EM: Association of
polymorphisms in the mast cell chymase gene promoter region (-1903
g/A) and (TG)n(GA)m repeat downstream of the gene with bronchial
asthma in children. J Investig Allergol Clin Immunol 2008, 18(5):376-381.
47. Imada Y, Fujimoto M, Hirata K, Hirota T, Suzuki Y, Saito H, Matsumoto K,
Akazawa A, Katsunuma T, Yoshihara S, Ebisawa M, Shibasaki M, Arinami T,
Tamari M, Noguchi E: Large scale genotyping study for asthma in the
Japanese population. BMC Res Notes 2009, 2:54.
48. Imboden M, Nicod L, Nieters A, Glaus E, Matyas G, Bircher AJ, Ackermann-
Liebrich U, Berger W, Probst-Hensch NM: The common G-allele of
interleukin-18 single-nucleotide polymorphism is a genetic risk factor for
atopic asthma. The SAPALDIA Cohort Study. Clin Exp Allergy 2006,
49. Islam T, Breton C, Salam MT, McConnell R, Wenten M, Gauderman WJ,
Conti D, Van Den Berg D, Peters JM, Gilliland FD: Role of inducible nitric
oxide synthase in asthma risk and lung function growth during
adolescence. Thorax 2009, 65(2):139-145.
50. Jaradat M, Stapleton C, Tilley SL, Dixon D, Erikson CJ, McCaskill JG, Kang HS,
Angers M, Liao G, Collins J, Grissom S, Jetten AM: Modulatory role for
retinoid-related orphan receptor alpha in allergen-induced lung
inflammation. Am J Respir Crit Care Med 2006, 174(12):1299-1309.
51. Jetten AM: Retinoid-related orphan receptors (RORs): critical roles in
development, immunity, circadian rhythm, and cellular metabolism. Nucl
Recept Signal 2009, 7:e003.
52. Koppelman GH, Meyers DA, Howard TD, Zheng SL, Hawkins GA,
Ampleford EJ, Xu J, Koning H, Bruinenberg M, Nolte IM, van Diemen CC,
Boezen HM, Timens W, Whittaker PA, Stine OC, Barton SJ, Holloway JW,
Holgate ST, Graves PE, Martinez FD, van Oosterhout AJ, Bleecker ER,
Postma DS: Identification of PCDH1 as a novel susceptibility gene for
bronchial hyperresponsiveness. Am J Respir Crit Care Med 2009,
53. Kowal K, Bodzenta-Lukaszyk A, Pampuch A, Szmitkowski M, Zukowski S,
Donati MB, Iacoviello L: Analysis of -675 4 g/5 G SERPINE1 and C-159T
CD14 polymorphisms in house dust mite-allergic asthma patients. J
Investig Allergol Clin Immunol 2008, 18(4):284-292.
54. Kowal K, Moniuszko M, Zukowski S, Bodzenta-Lukaszyk A: Concentrations
of plasminogen activator inhibitor-1 (PAI-1) and urokinase plasminogen
activator (uPA) in induced sputum of asthma patients after allergen
challenge. Folia Histochem Cytobiol 2010, 48(4):518-523.
55. Kucharewicz I, Mogielnicki A, Kasacka I, Buczko W, Bodzenta-Lukaszyk A:
Plasmin system regulation in an ovalbumin-induced rat model of
asthma. Int Arch Allergy Immunol 2008, 147(3):190-196.
56. Lee CC, Lin WY, Wan L, Tsai Y, Tsai CH, Huang CM, Chen CP, Tsai FJ:
Association of interleukin-18 gene polymorphism with asthma in
Chinese patients. J Clin Lab Anal 2008, 22(1):39-44.
57. Lee JH, Moore JH, Park SW, Jang AS, Uh ST, Kim YH, Park CS, Park BL,
Shin HD: Genetic interactions model among Eotaxin gene
polymorphisms in asthma. J Hum Genet 2008,
58. Li H, Romieu I, Sienra-Monge JJ, Ramirez-Aguilar M, Estela Del Rio-
Navarro B, Kistner EO, Gjessing HK, Lara-Sanchez Idel C, Chiu GY, London SJ:
Genetic polymorphisms in arginase I and II and childhood asthma and
atopy. J Allergy Clin Immunol 2006, 117(1):119-126.
59. Li YF, Tseng PJ, Lin CC, Hung CL, Lin SC, Su WC, Huang YL, Sung FC, Tai CK:
NAD(P)H: Quinone oxidoreductase 1, glutathione S-transferase M1,
environmental tobacco smoke exposure, and childhood asthma. Mutat
Res 2009, 678(1):53-58.
60. Liu Q, Xia Y, Zhang W, Li J, Wang P, Li H, Wei C, Gong Y: A functional
polymorphism in the SPINK5 gene is associated with asthma in a
Chinese Han Population. BMC Med Genet 2009, 10:59.
61. Madore AM, Perron S, Turmel V, Laviolette M, Bissonnette EY, Laprise C:
Alveolar macrophages in allergic asthma: an expression signature
characterized by heat shock protein pathways. Hum Immunol 2010,
62. Martinez B, Barrios K, Vergara C, Mercado D, Jimenez S, Gusmao L,
Caraballo L: A NOS1 gene polymorphism associated with asthma and
specific immunoglobulin E response to mite allergens in a Colombian
population. Int Arch Allergy Immunol 2007, 144(2):105-113.
63. Masumoto J, Yang K, Varambally S, Hasegawa M, Tomlins SA, Qiu S,
Fujimoto Y, Kawasaki A, Foster SJ, Horie Y, Mak TW, Nunez G,
Chinnaiyan AM, Fukase K, Inohara N: Nod1 acts as an intracellular
receptor to stimulate chemokine production and neutrophil recruitment
in vivo. J Exp Med 2006, 203(1):203-213.
64. Matsuzaki S, Ishizuka T, Hisada T, Aoki H, Komachi M, Ichimonji I, Utsugi M,
Ono A, Koga Y, Dobashi K, Kurose H, Tomura H, Mori M, Okajima F:
Lysophosphatidic acid inhibits CC chemokine ligand 5/RANTES
production by blocking IRF-1-mediated gene transcription in human
bronchial epithelial cells. J Immunol 2010, 185(8):4863-4872.
65. McKay A, Komai-Koma M, MacLeod KJ, Campbell CC, Kitson SM,
Chaudhuri R, Thomson L, McSharry C, Liew FY, Thomson NC: Interleukin-18
levels in induced sputum are reduced in asthmatic and normal smokers.
Clin Exp Allergy 2004, 34(6):904-910.
66. Millstein JCD, Gilliland FD, Gauderman WJ: A testing framework for
identifying suseptibility genes in the presence of epistasis. Am J Hum
Genet 2006, 78:15-27.
67. Minelli C, Granell R, Newson R, Rose-Zerilli MJ, Torrent M, Ring SM,
Holloway JW, Shaheen SO, Henderson JA: Glutathione-S-transferase genes
and asthma phenotypes: a Human Genome Epidemiology (HuGE)
systematic review and meta-analysis including unpublished data. Int J
Epidemiol 2010, 39(2):539-562.
68. Moller-Larsen S, Nyegaard M, Haagerup A, Vestbo J, Kruse TA, Borglum AD:
Association analysis identifies TLR7 and TLR8 as novel risk genes in
asthma and related disorders. Thorax 2008, 63(12):1064-1069.
69. Movahedi M, Moin M, Gharagozlou M, Aghamohammadi A, Dianat S,
Moradi B, Nicknam MH, Nikbin B, Amirzargar A: Association of HLA class II
alleles with childhood asthma and Total IgE levels. Iran J Allergy Asthma
Immunol 2008, 7(4):215-220.
70. Munthe-Kaas MC, Carlsen KH, Haland G, Devulapalli CS, Gervin K, Egeland T,
Carlsen KL, Undlien D: T cell-specific T-box transcription factor haplotype
is associated with allergic asthma in children. J Allergy Clin Immunol 2008,
71. Munthe-Kaas MC, Carlsen KL, Carlsen KH, Egeland T, Haland G,
Devulapalli CS, Akselsen H, Undlien D: HLA Dr-Dq haplotypes and the
TNFA-308 polymorphism: associations with asthma and allergy. Allergy
72. Nagase T, Kurihara H, Kurihara Y, Aoki-Nagase T, Nagai R, Ouchi Y:
Disruption of ET-1 gene enhances pulmonary responses to
methacholine via functional mechanism in knockout mice. J Appl Physiol
73. Nicolae D, Cox NJ, Lester LA, Schneider D, Tan Z, Billstrand C, Kuldanek S,
Donfack J, Kogut P, Patel NM, Goodenbour J, Howard T, Wolf R,
Koppelman GH, White SR, Parry R, Postma DS, Meyers D, Bleecker ER,
Hunt JS, Solway J, Ober C: Fine mapping and positional candidate studies
identify HLA-G as an asthma susceptibility gene on chromosome 6p21.
Am J Hum Genet 2005, 76(2):349-357.
74. Pampuch A, Kowal K, Bodzenta-Lukaszyk A, Di Castelnuovo A, Chyczewski L,
Donati MB, Iacoviello L: The -675 4G/5G plasminogen activator inhibitor-1
promoter polymorphism in house dust mite-sensitive allergic asthma
patients. Allergy 2006, 61(2):234-238.
75. Pegorier S, Arouche N, Dombret MC, Aubier M, Pretolani M: Augmented
epithelial endothelin-1 expression in refractory asthma. J Allergy Clin
Immunol 2007, 120(6):1301-1307.
76. Raby BA, Hwang ES, Van Steen K, Tantisira K, Peng S, Litonjua A, Lazarus R,
Giallourakis C, Rioux JD, Sparrow D, Silverman EK, Glimcher LH, Weiss ST: T-
bet polymorphisms are associated with asthma and airway
hyperresponsiveness. Am J Respir Crit Care Med 2006, 173(1):64-70.
77. Ray R, Choi M, Zhang Z, Silverman GA, Askew D, Mukherjee AB:
Uteroglobin suppresses SCCA gene expression associated with allergic
asthma. J Biol Chem 2005, 280(11):9761-9764.
78. Saadi A, Gao G, Li H, Wei C, Gong Y, Liu Q: Association study between
vitamin D receptor gene polymorphisms and asthma in the Chinese
Han population: a case-control study. BMC Med Genet 2009, 10:71.
79. Salam MT, Islam T, Gauderman WJ, Gilliland FD: Roles of arginase variants,
atopy, and ozone in childhood asthma. J Allergy Clin Immunol 2009,
123(3):596-602, 602 e591-598.
80. Sanz C, Isidro-Garcia M, Davila I, Moreno E, Laffond E, Lorente F: Analysis of
927T > C CYSLTRI and -444A > C LTC4S polymorphisms in patients with
asthma. J Investig Allergol Clin Immunol 2006, 16(6):331-337.
Melén et al. Respiratory Research 2011, 12:86
Page 9 of 10
81. Seibold MA, Reese TA, Choudhry S, Salam MT, Beckman K, Eng C, Atakilit A,
Meade K, Lenoir M, Watson HG, Thyne S, Kumar R, Weiss KB, Grammer LC,
Avila P, Schleimer RP, Fahy JV, Rodriguez-Santana J, Rodriguez-Cintron W,
Boot RG, Sheppard D, Gilliland FD, Locksley RM, Burchard EG: Differential
enzymatic activity of common haplotypic versions of the human acidic
Mammalian chitinase protein. J Biol Chem 2009, 284(29):19650-19658.
82. Suttner K, Rosenstiel P, Depner M, Schedel M, Pinto LA, Ruether A,
Adamski J, Klopp N, Illig T, Vogelberg C, Schreiber S, von Mutius E,
Kabesch M: TBX21 gene variants increase childhood asthma risk in
combination with HLX1 variants. J Allergy Clin Immunol 2009,
123(5):1062-1068, 1068 e1061-1068.
83. Szalai C, Kozma GT, Nagy A, Bojszko A, Krikovszky D, Szabo T, Falus A:
Polymorphism in the gene regulatory region of MCP-1 is associated
with asthma susceptibility and severity. J Allergy Clin Immunol 2001,
84. Szczepankiewicz A, Breborowicz A, Skibinska M, Wilkosc M, Tomaszewska M,
Hauser J: Association analysis of brain-derived neurotrophic factor gene
polymorphisms in asthmatic children. Pediatr Allergy Immunol 2007,
85. Szczepankiewicz A, Rose-Zerilli MJ, Barton SJ, Holgate ST, Holloway JW:
Association analysis of brain-derived neurotrophic factor gene
polymorphisms in asthmatic families. Int Arch Allergy Immunol 2009,
86. van den Oord RA, Sheikh A: Filaggrin gene defects and risk of developing
allergic sensitisation and allergic disorders: systematic review and meta-
analysis. Bmj 2009, 339 :b2433.
87. Wang J, Xu Y, Zhao H, Sui H, Liang H, Jiang X: Genetic variations in
chemoattractant receptor expressed on Th2 cells (CRTH2) is associated
with asthma susceptibility in Chinese children. Mol Biol Rep 2009,
88. Wang JY, Shyur SD, Wang WH, Liou YH, Lin CG, Wu YJ, Wu LS: The
polymorphisms of interleukin 17A (IL17A) gene and its association with
pediatric asthma in Taiwanese population. Allergy 2009, 64(7):1056-1060.
89. Vergara C, Tsai YJ, Grant AV, Rafaels N, Gao L, Hand T, Stockton M,
Campbell M, Mercado D, Faruque M, Dunston G, Beaty TH, Oliveira RR,
Ponte EV, Cruz AA, Carvalho E, Araujo MI, Watson H, Schleimer RP,
Caraballo L, Nickel RG, Mathias RA, Barnes KC: Gene encoding Duffy
antigen/receptor for chemokines is associated with asthma and IgE in
three populations. Am J Respir Crit Care Med 2008, 178(10):1017-1022.
90. White JH, Chiano M, Wigglesworth M, Geske R, Riley J, White N, Hall S,
Zhu G, Maurio F, Savage T, Anderson W, Cordy J, Ducceschi M, Vestbo J,
Pillai SG: Identification of a novel asthma susceptibility gene on
chromosome 1qter and its functional evaluation. Hum Mol Genet 2008,
91. Yamagata S, Tomita K, Sato R, Niwa A, Higashino H, Tohda Y: Interleukin-
18-deficient mice exhibit diminished chronic inflammation and airway
remodelling in ovalbumin-induced asthma model. Clin Exp Immunol 2008,
92. Yang CJ, Liu YK, Liu CL, Shen CN, Kuo ML, Su CC, Tseng CP, Yen TC,
Shen CR: Inhibition of acidic mammalian chitinase by RNA interference
suppresses ovalbumin-sensitized allergic asthma. Hum Gene Ther 2009,
93. Ye Q, Fujita M, Ouchi H, Inoshima I, Maeyama T, Kuwano K, Horiuchi Y,
Hara N, Nakanishi Y: Serum CC-10 in inflammatory lung diseases.
Respiration 2004, 71(5):505-510.
94. Zeilinger S, Pinto LA, Nockher WA, Depner M, Klopp N, Illig T, von Mutius E,
Renz H, Kabesch M: The effect of BDNF gene variants on asthma in
German children. Allergy 2009, 64(12):1790-1794.
95. Zheng XQ, Li CC, Xu DP, Lin A, Bao WG, Yang GS, Yan WH: Analysis of the
plasma soluble human leukocyte antigen-G and interleukin-10 levels in
childhood atopic asthma. Hum Immunol 2010, 71(10):982-987.
96. Zhou H, Hong X, Jiang S, Dong H, Xu X: Analyses of associations between
three positionally cloned asthma candidate genes and asthma or
asthma-related phenotypes in a Chinese population. BMC Med Genet
2009, 10 :123.
97. Haland G, Carlsen KC, Sandvik L, Devulapalli CS, Munthe-Kaas MC,
Pettersen M, Carlsen KH: Reduced lung function at birth and the risk of
asthma at 10 years of age. N Engl J Med 2006, 355(16):1682-1689.
98. Martinez FD, Wright AL, Taussig LM, Holberg CJ, Halonen M, Morgan WJ:
Asthma and wheezing in the first six years of life. The Group Health
Medical Associates. N Engl J Med 1995, 332(3):133-138.
99. Hunninghake GM, Cho MH, Tesfaigzi Y, Soto-Quiros ME, Avila L, Lasky-Su J,
Stidley C, Melen E, Soderhall C, Hallberg J, Kull I, Kere J, Svartengren M,
Pershagen G, Wickman M, Lange C, Demeo DL, Hersh CP, Klanderman BJ,
Raby BA, Sparrow D, Shapiro SD, Silverman EK, Litonjua AA, Weiss ST,
Celedon JC: MMP12, lung function, and COPD in high-risk populations. N
Engl J Med 2009, 361(27):2599-2608.
100. Maeda Y, Dave V, Whitsett JA: Transcriptional control of lung
morphogenesis. Physiol Rev 2007, 87(1):219-244.
101. Franzdottir SR, Axelsson IT, Arason AJ, Baldursson O, Gudjonsson T,
Magnusson MK: Airway branching morphogenesis in three dimensional
culture. Respir Res 2010, 11:162.
102. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS,
Manolio TA: Potential etiologic and functional implications of genome-
wide association loci for human diseases and traits. Proc Natl Acad Sci
USA 2009, 106(23):9362-9367.
103. Ting JP, Duncan JA, Lei Y: How the noninflammasome NLRs function in
the innate immune system. Science 2010, 327(5963):286-290.
104. Fagan KA, McMurtry IF, Rodman DM: Role of endothelin-1 in lung disease.
Respir Res 2001, 2(2):90-101.
105. Stow LR, Jacobs ME, Wingo CS, Cain BD: Endothelin-1 gene regulation.
FASEB J 2011, 25(1):16-28.
106. Kurihara Y, Kurihara H, Oda H, Maemura K, Nagai R, Ishikawa T, Yazaki Y:
Aortic arch malformations and ventricular septal defect in mice deficient
in endothelin-1. J Clin Invest 1995, 96(1):293-300.
107. Kurihara Y, Kurihara H, Suzuki H, Kodama T, Maemura K, Nagai R, Oda H,
Kuwaki T, Cao WH, Kamada N, et al: Elevated blood pressure and
craniofacial abnormalities in mice deficient in endothelin-1. Nature 1994,
108. Hocher B, Schwarz A, Fagan KA, Thone-Reineke C, El-Hag K, Kusserow H,
Elitok S, Bauer C, Neumayer HH, Rodman DM, Theuring F: Pulmonary
fibrosis and chronic lung inflammation in ET-1 transgenic mice. Am J
Respir Cell Mol Biol 2000, 23(1):19-26.
109. Immervoll T, Loesgen S, Dutsch G, Gohlke H, Herbon N, Klugbauer S,
Dempfle A, Bickeboller H, Becker-Follmann J, Ruschendorf F, Saar K, Reis A,
Wichmann HE, Wjst M: Fine mapping and single nucleotide
polymorphism association results of candidate genes for asthma and
related phenotypes. Hum Mutat 2001, 18(4):327-336.
110. Zhu G, Carlsen K, Carlsen KH, Lenney W, Silverman M, Whyte MK, Hosking L,
Helms P, Roses AD, Hay DW, Barnes MR, Anderson WH, Pillai SG:
Polymorphisms in the endothelin-1 (EDN1) are associated with asthma
in two populations. Genes Immun 2008, 9(1):23-29.
111. Melen E, Bruce S, Doekes G, Kabesch M, Laitinen T, Lauener R, Lindgren CM,
Riedler J, Scheynius A, van Hage-Hamsten M, Kere J, Pershagen G,
Wickman M, Nyberg F: Haplotypes of G protein-coupled receptor 154 are
associated with childhood allergy and asthma. Am J Respir Crit Care Med
2005, 171(10) :1089-1095.
Cite this article as: Melén et al.: Expression analysis of asthma candidate
genes during human and murine lung development. Respiratory Research
Submit your next manuscript to BioMed Central
and take full advantage of:
• Convenient online submission
• Thorough peer review
• No space constraints or color ﬁgure charges
• Immediate publication on acceptance
• Inclusion in PubMed, CAS, Scopus and Google Scholar
• Research which is freely available for redistribution
Submit your manuscript at
Melén et al. Respiratory Research 2011, 12:86
Page 10 of 10