Comparison of Proteomic and Transcriptomic Profiles in
the Bronchial Airway Epithelium of Current and Never
Katrina Steiling1,2*, Aran Y. Kadar3, Agnes Bergerat4, James Flanigon2, Sriram Sridhar4, Vishal Shah2, Q.
Rushdy Ahmad5, Jerome S. Brody1, Marc E. Lenburg1,2,4, Martin Steffen4, Avrum Spira1,2
1The Pulmonary Center, Boston University Medical Center, Boston, Massachusetts, United States of America, 2Bioinformatics Program, College of Engineering, Boston
University, Boston, Massachusetts, United States of America, 3Newton-Wellesley Hospital, Newton, Massachusetts, United States of America, 4Department of Pathology
and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America, 5The Broad Institute of Harvard and MIT, Cambridge,
Massachusetts, United States of America
Background: Although prior studies have demonstrated a smoking-induced field of molecular injury throughout the lung
and airway, the impact of smoking on the airway epithelial proteome and its relationship to smoking-related changes in the
airway transcriptome are unclear.
Methodology/Principal Findings: Airway epithelial cells were obtained from never (n=5) and current (n=5) smokers by
brushing the mainstem bronchus. Proteins were separated by one dimensional polyacrylamide gel electrophoresis (1D-
PAGE). After in-gel digestion, tryptic peptides were processed via liquid chromatography/ tandem mass spectrometry (LC-
MS/MS) and proteins identified. RNA from the same samples was hybridized to HG-U133A microarrays. Protein detection
was compared to RNA expression in the current study and a previously published airway dataset. The functional properties
of many of the 197 proteins detected in a majority of never smokers were similar to those observed in the never smoker
airway transcriptome. LC-MS/MS identified 23 proteins that differed between never and current smokers. Western blotting
confirmed the smoking-related changes of PLUNC, P4HB1, and uteroglobin protein levels. Many of the proteins differentially
detected between never and current smokers were also altered at the level of gene expression in this cohort and the prior
airway transcriptome study. There was a strong association between protein detection and expression of its corresponding
transcript within the same sample, with 86% of the proteins detected by LC-MS/MS having a detectable corresponding
probeset by microarray in the same sample. Forty-one proteins identified by LC-MS/MS lacked detectable expression of a
corresponding transcript and were detected in #5% of airway samples from a previously published dataset.
Conclusions/Significance: 1D-PAGE coupled with LC-MS/MS effectively profiled the airway epithelium proteome and
identified proteins expressed at different levels as a result of cigarette smoke exposure. While there was a strong correlation
between protein and transcript detection within the same sample, we also identified proteins whose corresponding
transcripts were not detected by microarray. This noninvasive approach to proteomic profiling of airway epithelium may
provide additional insights into the field of injury induced by tobacco exposure.
Citation: Steiling K, Kadar AY, Bergerat A, Flanigon J, Sridhar S, et al. (2009) Comparison of Proteomic and Transcriptomic Profiles in the Bronchial Airway
Epithelium of Current and Never Smokers. PLoS ONE 4(4): e5043. doi:10.1371/journal.pone.0005043
Editor: Carol Feghali-Bostwick, University of Pittsburgh, United States of America
Received November 21, 2008; Accepted February 15, 2009; Published April 9, 2009
Copyright: ? 2009 Steiling et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Doris Duke Charitable Foundation (AS), NIH/NCI R01CA124640 (AS and MEL), NIH/NIEHS U01ES016035 (AS and MEL), ATS Fellow Career Development
Award (KS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: email@example.com
Cigarette smoking, the leading cause of preventable death in
the United States, is responsible for 440,000 deaths per
year[1,2]. Smoking is the single most important risk factor in
the development of lung cancer, the leading cause of cancer
related death in the U.S., and of chronic obstructive pulmonary
disease (COPD), the fourth leading cause of death overall.
Although smoking is strongly associated with diseases such as
lung cancer and COPD, the mechanisms by which smoking
contributes to their pathogenesis are not completely understood.
Cigarette smoke creates a field of molecular injury in the
epithelial cells lining the entire respiratory tract. Changes include
cellular atypia, allelic loss[4–6], and promoter hypermethyla-
tion. Using oligonucleotide arrays and candidate gene ap-
proaches, our group and others have previously identified a
number of mRNA expression changes that occur in the
histologically normal airway epithelium in response to smok-
ing[8–12] and in association with disease[13–16]. Furthermore,
we have recently described smoking-induced changes in airway
microRNA expression and their potential role in regulating the
mRNA response to tobacco smoke . In this study, we sought to
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extend this field of molecular injury to the protein level and
characterize the effect of smoking on the airway epithelium
Prior studies have analyzed lung tissue from never, current and
former smokers using two-dimensional electrophoresis (2DE)
coupled with mass spectrometry, leading to the hypothesis that
smoke exposure induces an unfolded-protein-like response .
Other studies identified lung-cancer-specificproteomic differences in
bronchial epithelium obtained by biopsy from both ‘‘healthy’’
smokers and smokers with a history of lung cancer[19,20]. Though
studies have been performed using pooled nasal lavage samples
and pooled exhaled breath condensate samples, little is known
about either the effects of smoking on the proteome of airway
epithelial cells, or the variability inthis response between individuals.
In the current study we examined the effects of smoking on the
airway epithelial proteome by analyzing individual samples collected
by bronchoscopy from the mainstem bronchus. The ability to collect
variation in the proteomic response to cigarette smoke between
individuals which may ultimately be useful for determining why only
a subset of smokers develop lung cancer or COPD.
Although studies have tried to address the large-scale correla-
tion between protein production and mRNA expression in both
cell lines[23–39] and human tissues[40–46], the findings have
been variable. Studies of yeast and human liver tissue have yielded
moderate correlation of protein abundance to mRNA expres-
sion[23,36–38,43]. A strong correlation has been reported for
abundant proteins in an epithelial cell line model of ErbB-2
overproduction in breast cancer; however, protein abundance
and levels of mRNA expression have correlated poorly in resected
lung adenocarcinomas[45,46]. The relationship between protein
production and mRNA expression in normal airway epithelium
remains unclear, as does the impact of smoking on this
In this study, we profiled proteins and genes expressed within
the same bronchial epithelium of never and current smokers via
1D-PAGE with LC-MS/MS and DNA microarrays respectively.
The relationship between protein detection and mRNA expression
was explored both globally and for individual proteins of interest.
We found that the majority of airway proteins detected by mass
spectrometry have their corresponding transcripts detected at
measurable levels by microarray, and that changes at the protein
level in response to cigarette smoke parallel smoking-induced
changes in mRNA. This approach also detected proteins whose
corresponding transcript expression was not detected by micro-
arrays. This study represents the first application of this approach
to the simultaneous proteomic and transcriptomic profiling of
airway epithelium within the same individual, providing insight
into the normal and smoking-affected airway proteome and the
relationship between protein changes and the previously described
changes in airway gene expression.
The idemographics for subjects recruited into this study are
shown in Table 1. The never and current smokers differed in age
and cumulative tobacco exposure (as measured by pack-years of
smoking) (p,0.05), but were similar for other demographics. None
of the subjects were using inhaled medications.
Normal Airway Proteome
A total of 652 proteins were detected in one or more never
smokers, with 197 proteins found in the majority of never smokers
(Figure 1). Proteins with molecular functions related to airway
biology were over-represented among this list (Table 2). The
functional categorization of the normal airway proteome was
compared to over-represented functional categories of the normal
airway transcriptome among transcripts detected by microarray
both in these same five never smoker samples as well as a
larger previously described cohort of 22 never smokers .
mRNAs and proteins associated with nucleotide binding, and
pyrophosphate activity were over-represented in both datasets
Effect of Cigarette Smoking on the Large Airway
613 proteins were detected in one or more current smokers, and
169 proteins were detected in the majority of current smokers
(Figure 1). Three proteins differed in their rate of detection
between current and never smokers at PFisher#0.05. Aldehyde
dehydrogenase 3B1 (ALDH3B1, NP_000685), a gene highly
expressed in lung, was detected in all five never smokers and
only one current smoker (PFisher=0.048). Palate, lung and nasal
Table 1. Demographics of the 10 subjects undergoing bronchoscopy.
SampleAgeSex Cumulative Tobacco Exposure (Pack Years)FVC% FEV1% FEV1/FVC
NS1 23Male0 101%96%0.82
NS232Male0 88% 97%0.91
NS328 Male0 98%101% 0.87
NS432 Female0 108%111%0.89
NS527 Male0 127%140% 0.92
CS1 34Male17 87%84% 0.81
CS2 34Female15 84% 85%0.72
CS345 Female14 90%94%0.88
CS547 Male39.591% 89%0.81
NS indicates never smokers, and CS indicates current smokers. FVC indicates the forced vital capacity as a percent of the predicted value. FEV1% indicates the forced
expiratory volume at one second as a percent of the predicted value. A Student’s t-test was performed for continuous variables, and a chi square test for dichotomous
variables. Never and current smokers differed in age and pack years of smoking (p,0.05).
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epithelium carcinoma associated protein precursor (PLUNC,
NP_570913), a secretory protein in the upper respiratory tract
was detected in four never smokers and absent in all current
smokers (PFisher=0.048). Hypothetical protein DKFZP586A0522
protein (NP_054752) was also detected in four never smokers and
absent in all current smokers (PFisher=0.048).
Due to the small sample size, a second list of differentially
detected proteins was defined using a qualitative criterion: proteins
Figure 1. Venn diagram describing the proportion of proteins detected in never and current smokers. The circles represent proteins
detected in at least one sample. A total of 859 proteins were detected by LC-MS/MS in any sample. 652 proteins were detected by LC-MS/MS in any
never smoker, and 613 proteins were detected in at least one current smoker. The inner oval represents proteins detected by LC-MS/MS in the
majority of samples. 197 proteins were detected in the majority of never smokers, and 169 proteins were detected in the majority of current smokers.
*A total of 23 proteins differ between never and current smokers based on the criteria described in the methods.
Table 2. Enriched functions in the never smoker airway proteome.
Hydrolase activity, acting on acid anhydrides1.0*1025
Hydrolase activity, acting on acid anhydrides, in phosphorous-containing anhydrides9.6*1026
Nucleoside-triphosphate activity 8.4*1026
Oxidoreductase activity, acting on the Aldehyde or oxo Group of donors7.0*1025
Oxidoreductase activity, acting on the Aldehyde or oxo group of donors, NAD or NADP as acceptor3.3*1025
Statistically enriched functional categories (FDR,0.05) and subcategories of the 197 proteins detected in the majority of never smokers as determined by DAVID. Over-
represented categories that contain more than two probe sets are included. Functional categories that are also over-represented (FDR,0.05) among transcripts
detected in the all never smokers in this cohort are bolded. Functional categories that are also enriched (FDR,0.05) among transcripts detected in all never smokers
from a previously published cohort  are italicized.
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were included if present in three or more samples of one class
compared to the other. Twenty-three proteins differed between
never and current smokers based on these criteria (Table 3).
We validated mass spectrometry findings by immunoblot for
three of the proteins that differed between never and current
smokers (Figure 2). PLUNC, uteroglobin and P4HB were selected
from the list of twenty-three candidates based on their biologic
interest, molecular weight, and antibody availability. Of these,
PLUNC also had a Fisher exact p-value,0.05. Decreased levels of
PLUNC and uteroglobin were confirmed among current smokers,
although there was heterogeneity for uteroglobin among current
smokers (Figure 2). P4HB levels were elevated in two of the current
smokers as compared to two never smokers.
Comparison of Protein and mRNA Expression
An average of 93% of proteins detected by mass spectrometry
had at least one matching probe set on the HG-U133A array. Of
these, an average of 86% had detectable gene expression
(Pdetection,0.05) in samples collected from the same participants
demonstrating a significant level of co-detection (x2=347,
p=2.2610216). There was not a significant difference in the rate
of co-detection between never and current smokers.
For select proteins where detection varied between never and
current smokers, we examined the expression of the corresponding
mRNA for smoking-related differential expression. PLUNC
(NP_570913), ALDH3B1 (NP_000685), and hypothetical protein
DKFZP586A0522 (NP_054752) were selected based on the results
of the Fisher exact test. Uteroglobin (NP_003348) and the prolyl 4-
hydroxylase beta subunit (P4HB) (NP_000909) were selected
based on their qualitative differences between never and current
smokers. Within this cohort, mRNA expression positively
correlated with protein detection for PLUNC, uteroglobin, and
P4HB (Figure 3).
The association between smoking and gene expression was also
examined in a previously published cohort  from which we
excluded a sample that overlapped with the samples used in this
study (Figure 3). Consistent with the protein detection data and the
gene expression data from the present study, in this independent
group of never and current smokers, ALDH3B1, hypothetical protein
DKFZP586A0522, PLUNC and uteroglobin mRNA expression were
higher in never smokers and P4HB gene expression was higher in
current smokers. Additionally, we used this cohort to assess the
potential confounding effects of age on the smoking-induced
changes in candidate proteins identified in the current study.
Within the previously published cohort, we identified 12 never and
12 current smokers matched within 1 year for age. A t-test
performed on these age-matched 12 never smokers and 12 current
smokers confirmed differential gene expression of ALDH3B1
(207761_s_at, p=0.03), PLUNC (220542_s_at, p=0.02), uteroglobin
(205725_at, p=0.0005), and P4HB1 (200654_at, p=0.03).
Table 3. Proteins differentially detected in the airway of never and current smokers by mass spectrometry.
Protein NameRefSeqID#Nevers / #Currents
transferrin; PRO2086 proteinNP_0010540/3
ribosomal protein S2; 40S ribosomal protein S2NP_002943 1/4
superoxide dismutase 2, mitochondrialNP_0006272/5
prolyl 4-hydroxylase, beta subunitNP_0009092/5
aldehyde dehydrogenase 9A1NP_000687 3/0
dynein, axonemal, heavy polypeptide 5NP_001360 3/0
dynein, axonemal, heavy polypeptide 9 isoform 2NP_001363 3/0
dynein, cytoplasmic, heavy polypeptide 1NP_0013673/0
prostatic binding protein NP_002558 3/0
phosphoglycerate mutase 1 (brain)NP_0026203/0
secretoglobin, family 1A, member 1 (uteroglobin)NP_0033483/0
Fc fragment of IgG binding proteinNP_0038813/0
aminopeptidase puromycin sensitiveNP_006301 3/0
arachidonate 15-lipoxygenaseNP_001131 4/1
S100 calcium binding protein A11NP_0056114/1
palate, lung and nasal epithelium carcinoma associated protein precursorNP_5709134/0
tubulin beta MGC4083 NP_1159145/2
aldehyde dehydrogenase 3B1NP_000685 5/1
The proteins that are differentially detected in never and current smokers are listed by protein name and by RefSeq identification number. The right column shows the
numbers of never and current smokers samples in which the protein was detected. Proteins with a Fisher exact p#0.05 comparing never and current smokers are
shown in bold.
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Differences in protein detection by mass spectrometry and
transcript detection by microarray were also explored. In the
matched samples, there was no expression by microarray of
transcripts corresponding to 41 proteins that were detected in
$50% of samples by mass spectrometry (Table 4). Additionally,
expression of these transcripts was detected in #5% of the never
and current smokers in the larger previously published dataset
of never and current smokers. Ten of these 41 proteins have been
previously described in the erythrocyte proteome, which is not
surprising given that brushings contain small numbers of red blood
cells that lack nucleic acids.
We applied 1D-PAGE coupled with LC-MS/MS to the study of
the airway epithelium proteome and its response to cigarette
smoke exposure. This study presents the first proteomic profile of a
relatively pure population of bronchial epithelial cells obtained
from bronchoscopy brushings. We also used differences in the rate
of protein detection between never and current smokers to identify
candidates for proteins that vary in abundance in response to
tobacco-smoke exposure. The effect of smoking on several of these
proteins was confirmed by Western blot. We also found that for
many candidates, smoking similarly affected expression of the
mRNA transcripts that gave rise to these proteins. This was
accomplished by measuring gene expression in the same samples
that were profiled at the proteomic level and in an independent
data set. The majority of proteins identified by LC-MS/MS had
detectable levels of their corresponding transcript by microarray.
Differing methodologies may account for the stronger relationship
between protein and gene expression reported here relative to
Analysis of the proteome using 1D-PAGE coupled with LC-
MS/MS resulted in the detection of 41 proteins for which
expression of corresponding transcripts was not detected by
microarray. Some of these failures to detect transcript expression
could represent technical limitations of the microarray platform.
However, we were intrigued that several of the proteins whose
transcripts were not detected by microarray represent erythrocyte-
specific proteins. This suggests that: 1) the airway epithelial
samples collected for this study were likely contaminated with
erythrocytes, and 2) that more generally, stable proteins may be
detected by proteomic methods long after the mRNA which
encodes for them has disappeared.
Using habitual smoking as a paradigm for inhalational
exposures affecting airway epithelium, we have identified changes
in protein among smokers by LC-MS/MS and validated select
changes with Western blotting. A decrease in the short isoform of
PLUNC has previously been described in the pooled nasal lavage
fluid of current smokers when compared with nonsmokers.
Although the exact function of this protein is unclear, it is thought to
act in the inflammatory response to inhaled irritants such as tobacco
smoke. Other studies have demonstrated decreased levels of
uteroglobin, an anti-inflammatory protein secreted by Clara cells,
in the BAL, pooled nasal lavage fluid, and serum of
healthy smokers and in the bronchial epithelium of former smokers
with COPD undergoing lung transplantation. P4HB has been
detected in a proteomic analysis of cell surface proteins of a lung
adenocarcinoma cell line and in the 2DE-proteomic analysis of
resected lung adenocarcinomas. This protein may function in
the anti-oxidant response to cigarette smoke. Other proteins
with oxidoreductase activity identified by this approach, such as
ALDH3B1, have not previously been linked to cigarette smoking at
the toxins in cigarette smoke. None of the proteins differentially
detected in smokers in this study overlapped with proteins previously
described as differentially expressed in the lungs of Winstar rats
exposed to cigarette smoke, or proteins differentially detected by
2DE/MALDI-TOF in a human pneumocyte cell line exposed to
cigarette smoke extract.
This study was limited by a relatively small sample size, the
sensitivity of the proteomic technique, and challenges in the
quantification of proteins. While age was a confounding variable
in this study, the gene expression changes in the airway epithelium
of never and current smokers were validated using age-matched
samples from current and never smokers in a previously published
gene-expression study , suggesting that the association between
smoking-status and both gene and protein expression is unlikely to
be due to differences in patient age. The amount of time elapsed
between last smoking a cigarette and bronchoscopy was not
recorded, and some of the variability of protein levels in Western
blotting might relate to potential differences to the acute versus
chronic effects of cigarette smoke. Although the small sample size
limited the statistical analysis, Western blotting validated differ-
ences in protein detection identified by LC-MS/MS suggesting the
method’s potential specificity. However, the power of our study to
detect additional proteomic changes that occurred in response to
cigarette smoke exposure was limited. The sensitivity of this
technology allowed detection of 859 proteins with a false positive
rate of 1%. While this represents a small percentage of the total
proteins present in epithelial cells, we have identified a greater
number of proteins than previously used methods of sample
collection and proteomic analysis for smokers and nonsmok-
ers[20–22]. Because of the uncertainties associated with label-free
quantification methods for the determination of protein expression
levels, this platform serves mainly as a discovery tool. However,
promising efforts in this area, including correlation of peak
intensity or spectral counts with protein abundance, may soon
remove this limitation[55–58].
In summary, we have described the proteomic profile of normal
bronchial epithelial cells using 1D-PAGE coupled with LC-MS/
Figure 2. Western blot validation of proteins detected by
proteomics in never and current smokers. Western blotting shows
significantly higher levels of PLUNC in the never smokers. Higher levels
of uteroglobin were also observed in never smokers, although there
was heterogeneity among the current smokers. There was a small
increase in P4HB in two of the current smoker samples.
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MS and linked this profile to smoking-induced transcriptional
changes in these same cells. This approach has the potential to
provide additional insight into host response to tobacco smoke and
the pathogenesis of smoking-related lung disease.
Materials and Methods
Study population, sample collection, and ethics
Never (n=5) and current smokers (n=5) were recruited for
fiberoptic bronchoscopy at Boston Medical Center. Detailed
medical and smoking histories were obtained including number of
cigarettes smoked per day, cumulative tobacco exposure measured
in pack-years, and an estimation of second-hand smoke exposure.
Screening prior to bronchoscopy included an electrocardiogram,
chest radiograph and spirometry. Participants with a history of
underlying lung disease, significant second hand smoke exposure,
an abnormal baseline EKG, or evidence of obstructive lung
disease on spirometry (defined as an FEV1/FVC,0.7) were
excluded from the study. This study was approved by the
Institutional Review Board at Boston Medical Center, and all
subjects provided written informed consent.
Figure 3. Comparison of individual protein detection and mRNA expression. Boxplots of the gene expression levels and bar graphs of LC-
MS/MS results for A) ALDH3B1, B) hypothetical protein DKFZP586A0522, C) PLUNC, D) uteroglobin (CC10), and E) P4HB subunit. The borders of each
boxplot represent the interquartile range of z-score normalized natural logarithm of the MAS5 gene expression data from this cohort of 5 never
smoker and 5 current smokers, and from a previously published cohort (AGED) of 23 never smokers and 34 current smokers, excluding one never
smoker in common to this study. The solid line within each box represents the median gene expression, and the whiskers of the plot extend to the
upper and lower extremes of the data for each gene. Bar plots represent the number of smoker and nonsmoker samples in the current study where
the protein was detected. Proteomic analysis detected ALDH3B1, hypothetical protein DKFZP586A0522, PLUNC and uteroglobin in more never
smokers, while P4HB was detected in more current smokers. There is concordance in the direction of change for smoking-related protein and gene
expression changes for these 5 genes. * p,0.05. ** p,0.005. *** p,0.0005.
Table 4. Proteins detected in the airway by mass spectrometry that lack detectable transcript by microarray.
Protein Name (RefSeqID)
Actin, alpha 1, skeletal muscle (NP_001091)1,3
Succinate dehydrogenase complex, subunit B, iron sulfur (Ip) (NP_002991)5
Myosin, heavy polypeptide 14 (NP_079005)1,3
Superoxide dismutase 2, mitochondrial (NP_000627)5
Tubulin, beta 1 (NP_110400)1,3
Phosphorylase, glycogen; brain (NP_002853)6
Tubulin, beta 4 (NP_006078)1,3
Phosphorylase, glycogen; muscle (McArdle syndrome, glycogen storage disease type V)
Spectrin, alpha, non-erythrocytic 1 (alpha fodrin) (NP_003118)1,2,3,4
3-hydroxyisobutyrate dehydrogenase (NP_689953)8
Spectrin, beta, non-erythrocytic 1 (NP_842565)1,2,3,4
Adenylate kinase 1 (NP_000467)8,9
Villin 2 (ezrin) (NP_003370)1,2,3,4
N-acylsphingosine amidohydrolase (acid ceramidase) 1 (NP_808592)8
Histone 1, H1b (NP_005313)1
Apolipoprotein A-I (NP_000030)8
Histone 1, H3f (NP_066298)1
Cytochrome c oxidase subunit IV isoform 1 (NP_001852)8
Histone 1, H4k (NP_068803)1
Heat shock 70 kDa protein 1-like (NP_005518)8
RAB6A, member RAS oncogene family (NP_002860)1
Heat shock 70 kDa protein 6 (HSP70B9) (NP_002146)8
Heterogeneous nuclear ribonucleoprotein C (C1/C2) (NP_112604)8
Karyopherin (importin) beta 1 (NP_002256)1,5
Heterogeneous nuclear ribonucleoprotein M (NP_005959)8
Lamin A/C (NP_733821)3
Peptidylprolyl isomerase A (cyclophilin A) (NP_066953)8,9
Lamin B2 (NP_116126)3
Peroxiredoxin 2 (NP_005800)8,9
Phosphoglycerate kinase 1 (NP_000282)8
Carbonic anhydrase I (NP_001729)5,9
Pyruvate kinase, muscle (NP_002645)8
Carbonic anhydrase II (NP_000058)5,9
Solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band
3, Diego blood group) (NP_000033)8
Tumor rejection antigen (gp6) 1 (NP_003290)8
Hemoglobin, delta (NP_000510)5,7,9
Voltage-dependent anion channel 3 (NP_005653)8
Hemoglobin, gamma A (NP_000550)5,7,9
A total of 41 proteins detected in at least half of the samples by LC/MS-MS lacked detectable expression by microarray at a detection p-value,0.05. Fewer than 5% of
airway samples from a previously published dataset had detectable expression of a transcript corresponding to these proteins.
1Cell organization and biosynthesis (PDAVID,0.05).
2Cortical cytoskeleton (PDAVID,0.05).
4Cell cortex (PDAVID,0.05).
5Transition metal ion binding (PDAVID,0.05).
6Pyridoxal phosphate binding (PDAVID,0.05).
7Oxygen binding (PDAVID,0.05).
8Unclassified in DAVID.
9Component of the erythrocyte proteome .
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Bronchial epithelial cell brushings from the right mainstem
bronchus were obtained at the time of bronchoscopy with an
endoscopic cytology brush (Cellebrity Endoscopic Cytology Brush,
Boston Scientific, Natick, MA). Cytokeratin staining has demon-
strated that this method results in the collection of greater than
90% pure population of bronchial epithelial cells. Airway
brushings obtained for proteomics were immediately placed in
PBS (Invitrogen, Carlsbad, CA). Additional brushes were collected
for gene expression profiling and stored in TRIzol (Invitrogen).
Samples in PBS were pelletted at 3500 rpm for 3 minutes, washed
with PBS, and stored at 280uC until processing for mass
spectrometry. The airway brushings in TRIzol were stored at
280uC until processing.
Proteomic Sample Processing and Mass Spectrometry
After cell lysis with 2% SDS, proteins were separated on a 4–
20% polyacrylamide minigel by electrophoresis and stained with
Coomassie Blue (Supporting Figure S1). Each gel lane was cut into
35–70 sections. Proteins were reduced with DTT, alkylated with
iodoacetamide, and digested with trypsin using a DigestPro 96
robot (Intavis Bioanalytical Instruments, Cologne, Germany).
Extracted peptides were dried and resuspended in 0.5% acetic
acid in preparation for mass spectrometry.
All samples were analyzed by LC-MS/MS using an LTQ
ProteomeX ion trap mass spectrometer (ThermoFinnigan, Wal-
tham, MA). Peptides from each gel slice were serially injected onto
a home-packed C18 reverse-phase column (Magic C18AQ,
15 cm6100 micron ID, Michrom Bioresources, Inc., Auburn,
CA) interfaced directly to the mass spectrometer. Peptides were
separated using short, biphasic, 20-minute gradients of 0–90%
acetonitrile in the presence of 0.5% acetic acid. From each parent
ion scan (MS scan), the ten most intense ions were selected for
collision-induced dissociation, and the spectra of the peptide
fragments were recorded (MS2 scan).
Protein Identification and Analysis
The data were analyzed using SEQUEST software. Spectra
were queried against the curated entries of the NCBI RefSeq
database and Xcorr values adjusted for an empiric false positive
identification rate of 1% for forward-sequence proteins as
determined by the inclusion of reversed protein sequences.
Positive identification of a protein required observation of at least
two matching peptides from the same or adjacent gel slices.
Residual protein lysates from two never and five current smoker
samples were quantified by 1D-PAGE and Coomassie blue
staining (Supporting Figure S2). Of these samples, sufficient
material was available for Western blotting of two never smoker
samples and four current smoker samples. One current smoker
sample was excluded due to lack of signal from the loading control,
lamin A/C. Samples were incubated at 86uC in SDS-sample
buffer and electrophoresed on a 4–20% SDS-PAGE gel. Proteins
were transferred to nitrocellulose and stained with Ponceau Red.
The membrane was blocked with 5% nonfat milk in TBS-Tween
and incubated with the appropriate primary and secondary
antibodies. Mouse anti-human prolyl 4-hydroxylase beta subunit
was obtained from Chemicon (Temecula, CA). Mouse anti-human
PLUNC and goat anti-mouse-HRP affinity purified antibodies
were purchased from R&D Systems (Minneapolis, MN). Rabbit
anti-uteroglobin was obtained from Abcam (Cambridge, MA).
Lamin A/C, a nuclear matrix protein, was used as a loading
Microarray Sample Processing
Six to eight micrograms of RNA obtained from five of the never
smoker and four of the current smoker participants was processed
and hybridized to an Affymetrix HG-U133A GeneChip (Affyme-
trix Inc., Santa Clara, CA) containing ,22,215 probesets as
Microarray Data Acquisition and Preprocessing
Expression Console Version 1.0 (Affymetrix Inc.) was used to
generate a MAS5 weighted-mean expression level for each
transcript and a detection p-value (Pdetection), which indicates the
reliability of detection of that transcript above background on the
array. The mean intensity for each array was scaled to 100. Each
array included in the final analysis had at least 30% of the
probesets detected above background (percent present .30%) and
a 39 to 59 ratio of signal intensity for GAPDH of less than or equal
to 5. One never smoker microarray was excluded based on these
quality control filters (low percent present, high 39 to 59 GAPDH
ratio), leaving four never and four current smoker arrays for
Sample contamination with significant numbers of non-
epithelial cells was evaluated, as described previously, by
analyzing arrays for the presence of transcripts known to be
present in airway epithelium and by confirming the absence of
transcripts specific to non-epithelial cell types. No arrays were
excluded based on these criteria.
Comparison of Protein Detection and mRNA Expression
For each protein, we queried the microarray data from the same
patient for expression (Pdetection,0.05) of a matching transcript.
The significance of the overlap between detected proteins and
transcripts was determined using Pearson’s Chi-squared test with
Yates’ continuity correction.
A comparison of protein detection and transcript expression
level was also performed for individual proteins of interest using
the microarray data generated in this study and a previously
published cohort of 23 never smokers and 34 current smokers ,
excluding one never smoker in common to this cohort. The
transcript expression data for these samples was obtained from
http://pulm.bumc.bu.edu/aged and log normalized. The associ-
ation between smoking status and gene expression was determined
as previously described .
Functional Enrichment Analysis
Functional enrichment analysis was performed using DAVID
(http://david.abcc.ncifcrf.gov/). A modified Fisher exact test
method was used to correct for false discovery (PDAVID-BH).
To determine the molecular functions that were over-represented
within the never smoker proteome, the Gene Ontology (GO)
molecular functions of the U133A probes corresponding to the
proteins detected in the majority of never smokers were compared to
the GO molecular functions of all probe sets on the U133A array. A
similar analysis was also performed for the never smoker transcrip-
tome. Genes expressed at Pdetection,0.05 in all never smokers with
represented by probe sets on the U133A microarray. A parallel
analysis was performed in DAVID using the genes expressed at
Pdetection,0.05 in the 22 unique never smokers from a previously
published data set. Over-represented gene ontology categories for
proteins changed by smoking and for proteins that were not
detectably expressed by microarray were determined by comparing
the corresponding RefSeq identifications numbers for these proteins
Airway Proteomics in Smoking
PLoS ONE | www.plosone.org8 April 2009 | Volume 4 | Issue 4 | e5043
against the complete set of 859 proteins detected by mass
spectrometry in this set of experiments.
Additional information, including clinical data for all of the
study participants, the complete list of proteins detected in each
sample, percent peptide coverage for each protein and the
expression levels for all genes in all samples are stored in a
relational MYSQL database that is available at http://pulm.
bumc.bu.edu/parce/parce.html. Microarray data from this study
has been deposited in the National Center for Biotechnology
Information Gene Expression Omnibus (GSE4635). Proteomic
data has been deposited at Proteome Commons (http://www.
spectrometry. Proteins from each sample were separated by 1D-
PAGE prior to mass spectrometry. A representative sample is
shown. MW indicates the molecular weight marker. BSA indicates
a bovine serum albumin standard. CS indicates current smoker.
Found at: doi:10.1371/journal.pone.0005043.s001 (2.28 MB TIF)
1D-PAGE of a current smoker sample prior to mass
Western Blot. A small amount of material from each sample was
1D-PAGE for approximation of protein yield prior to
retained for Western blotting. To roughly normalize the protein
contribution from each sample, a small amount of material from
the remaining samples were analyzed on 1D-PAGE and stained
with Coomassie blue. MW indicates a molecular weight standard.
NS indicates never smokers, and CS indicates current smokers.
Found at: doi:10.1371/journal.pone.0005043.s002 (2.04 MB TIF)
The authors thank Yves-Martine Dumas for her assistance with sample
Conceived and designed the experiments: JB MS AS. Performed the
experiments: AB. Analyzed the data: KS JF QRA ML. Contributed
reagents/materials/analysis tools: JF SS VS QRA. Wrote the paper: KS JB
ML. Coordinated the study: KS. Performed the data analysis: KS. Was
responsible for protein isolation, proteomic analyses, and Western blotting:
AB. Was responsible for creation of the relational database: JF.
Contributed to the development of the relational database: SS VS. Wrote
custom software for and participated in proteomic data analysis: QRA.
Contributed to the study design: AYK JB. Contributed to the writing of the
manuscript: AYK JB ML. Contributed to the data analysis: JF ML.
Contributed to conception of the study and design of the proteomics
experiments: MS. Conceived the study and oversaw all aspects of the study:
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