Pulmonary Center Papers

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Role of Free Radicals in the Pathogenesis of Acute Chest Syndrome in Sickle Cell Disease
(BioMed Central, 2001-7-13) Klings, Elizabeth S.; Farber, Harrison W.
Acute chest syndrome (ACS) of sickle cell disease (SCD) is characterized pathologically by vaso-occlusive processes that result from abnormal interactions between sickle red blood cells (RBCs), white blood cells (WBCs) and/or platelets, and the vascular endothelium. One potential mechanism of vascular damage in ACS is by generation of oxygen-related molecules, such as superoxide (O2-), hydrogen peroxide (H2O2), peroxynitrite (ONOO-), and the hydroxyl (•OH) radical. The present review summarizes the evidence for alterations in oxidant stress during ACS of SCD, and the potential contributions of RBCs, WBCs and the vascular endothelium to this process.
Growth Factors in Lung Development and Disease: Friends or Foe?
(BioMed Central, 2001-10-9) Desai, Tushar J.; Cardoso, Wellington V.
Growth factors mediate tissue interactions and regulate a variety of cellular functions that are critical for normal lung development and homeostasis. Besides their involvement in lung pattern formation, growth and cell differentiation during organogenesis, these factors have been also implicated in modulating injury-repair responses of the adult lung. Altered expression of growth factors, such as transforming growth factor β1, vascular endothelial growth factor and epidermal growth factor, and/or their receptors, has been found in a number of pathological lung conditions. In this paper, we discuss the dual role of these molecules in mediating beneficial feedback responses or responses that can further damage lung integrity; we shall also discuss the basis for their prospective use as therapeutic agents.
RNAi Targeting of West Nile Virus in Mosquito Midguts Promotes Virus Diversification
(Public Library of Science, 2009-7-3) Brackney, Doug E.; Beane, Jennifer E.; Ebel, Gregory D.
West Nile virus (WNV) exists in nature as a genetically diverse population of competing genomes. This high genetic diversity and concomitant adaptive plasticity has facilitated the rapid adaptation of WNV to North American transmission cycles and contributed to its explosive spread throughout the New World. WNV is maintained in nature in a transmission cycle between mosquitoes and birds, with intrahost genetic diversity highest in mosquitoes. The mechanistic basis for this increase in genetic diversity in mosquitoes is poorly understood. To determine whether the high mutational diversity of WNV in mosquitoes is driven by RNA interference (RNAi), we characterized the RNAi response to WNV in the midguts of orally exposed Culex pipiens quinquefasciatus using high-throughput, massively parallel sequencing and estimated viral genetic diversity. Our data demonstrate that WNV infection in orally exposed vector mosquitoes induces the RNAi pathway and that regions of the WNV genome that are more intensely targeted by RNAi are more likely to contain point mutations compared to weakly targeted regions. These results suggest that, under natural conditions, positive selection of WNV within mosquitoes is stronger in regions highly targeted by the host RNAi response. Further, they provide a mechanistic basis for the relative importance of mosquitoes in driving WNV diversification. Author SummaryWest Nile virus (WNV) was introduced into New York state in 1999 and has since spread across the Americas. It is transmitted in nature between adult female mosquitoes and birds and occasionally infects humans and horses. Within the host, WNV exists as a diverse assortment of closely related mutants. WNV populations within mosquitoes are more complex genetically than are those within birds. The reasons for this discrepancy are unknown, but may be related to the host's innate antivirus response. We demonstrate that WNV is targeted by RNA interference, a highly sequence-specific pathway in the mosquito. Further, we present data that correlates the intensity of this targeting with virus mutation under natural conditions. These results provide a mechanistic explanation for the increasead complexity of WNV populations in mosquitoes: the RNAi response creates an intracellular environment where rare genotypes are favored. In addition, our results suggest that genetically diverse WNV populations may have an advantage over less diverse populations because they present a more complex target for the RNAi response. Finally, these data suggest that WNV, and possibly other viruses with high mutation rates, may escape an engineered antivirus intervention that is highly sequence-specific.
Orally Available Mn Porphyrins with Superoxide Dismutase and Catalase Activities
(Springer-Verlag, 2009-6-6) Rosenthal, Rosalind A.; Huffman, Karl D.; Fisette, Leslie W.; Damphousse, Christy A.; Callaway, Wyeth B.; Malfroy, Bernard; Doctrow, Susan R.
Superoxide dismutase/catalase mimetics, such as salen Mn complexes and certain metalloporphyrins, catalytically neutralize reactive oxygen and nitrogen species, which have been implicated in the pathogenesis of many serious diseases. Both classes of mimetic are protective in animal models of oxidative stress. However, only AEOL11207 and EUK-418, two uncharged Mn porphyrins, have been shown to be orally bioavailable. In this study, EUK-418 and several new analogs (the EUK-400 series) were synthesized and shown to exhibit superoxide dismutase, catalase, and peroxidase activities in vitro. Some also protected PC12 cells against staurosporine-induced cell death. All EUK-400 compounds were stable in simulated gastric fluid, and most were substantially more lipophilic than the salen Mn complexes EUK-189 and EUK-207, which lack oral activity. Pharmacokinetics studies demonstrate the presence of all EUK-400 series compounds in the plasma of rats after oral administration. These EUK-400 series compounds are potential oral therapeutic agents for cellular damage caused by oxidative stress. ELECTRONIC SUPPLEMENTARY MATERIAL. The online version of this article (doi:10.1007/s00775-009-0550-4) contains supplementary material, which is available to authorized users.
An Integration of Complementary Strategies for Gene-Expression Analysis to Reveal Novel Therapeutic Opportunities for Breast Cancer
(BioMed Central, 2009-7-28) Bild, Andrea H.; Parker, Joel S.; Gustafson, Adam M.; Acharya, Chaitanya R.; Hoadley, Katherine A.; Anders, Carey; Marcom, P. Kelly; Carey, Lisa A.; Potti, Anil; Nevins, Joseph R.; Perou, Charles M.
INTRODUCTION. Perhaps the major challenge in developing more effective therapeutic strategies for the treatment of breast cancer patients is confronting the heterogeneity of the disease, recognizing that breast cancer is not one disease but multiple disorders with distinct underlying mechanisms. Gene-expression profiling studies have been used to dissect this complexity, and our previous studies identified a series of intrinsic subtypes of breast cancer that define distinct populations of patients with respect to survival. Additional work has also used signatures of oncogenic pathway deregulation to dissect breast cancer heterogeneity as well as to suggest therapeutic opportunities linked to pathway activation. METHODS. We used genomic analyses to identify relations between breast cancer subtypes, pathway deregulation, and drug sensitivity. For these studies, we use three independent breast cancer gene-expression data sets to measure an individual tumor phenotype. Correlation between pathway status and subtype are examined and linked to predictions for response to conventional chemotherapies. RESULTS. We reveal patterns of pathway activation characteristic of each molecular breast cancer subtype, including within the more aggressive subtypes in which novel therapeutic opportunities are critically needed. Whereas some oncogenic pathways have high correlations to breast cancer subtype (RAS, CTNNB1, p53, HER1), others have high variability of activity within a specific subtype (MYC, E2F3, SRC), reflecting biology independent of common clinical factors. Additionally, we combined these analyses with predictions of sensitivity to commonly used cytotoxic chemotherapies to provide additional opportunities for therapeutics specific to the intrinsic subtype that might be better aligned with the characteristics of the individual patient. CONCLUSIONS. Genomic analyses can be used to dissect the heterogeneity of breast cancer. We use an integrated analysis of breast cancer that combines independent methods of genomic analyses to highlight the complexity of signaling pathways underlying different breast cancer phenotypes and to identify optimal therapeutic opportunities.
Production of IL-16 Correlates with CD4+ Th1 Inflammation and Phosphorylation of Axonal Cytoskeleton in Multiple Sclerosis Lesions
(BioMed Central, 2006-5-26) Skundric, Dusanka S.; Cai, Juan; Cruikshank, William W.; Gveric, Djordje
BACKGROUND Multiple sclerosis (MS) is a central nervous system-specific autoimmune, demyelinating and neurodegenerative disease. Infiltration of lesions by autoaggressive, myelin-specific CD4+Th1 cells correlates with clinical manifestations of disease. The cytokine IL-16 is a CD4+ T cell-specific chemoattractant that is biased towards CD4+ Th1 cells. IL-16 precursor is constitutively expressed in lymphocytes and during CD4+ T cell activation; active caspase-3 cleaves and releases C-terminal bioactive IL-16. Previously, we used an animal model of MS to demonstrate an important role for IL-16 in regulation of autoimmune inflammation and subsequent axonal damage. This role of IL-16 in MS is largely unexplored. Here we examine the regulation of IL-16 in relation to CD4+ Th1 infiltration and inflammation-related changes of axonal cytoskeleton in MS lesions. METHODS We measured relative levels of IL-16, active caspase-3, T-bet, Stat-1 (Tyr 701), and phosphorylated NF(M+H), in brain and spinal cord lesions from MS autopsies, using western blot analysis. We examined samples from 39 MS cases, which included acute, subacute and chronic lesions, as well as adjacent, normal-appearing white and grey matter. All samples were taken from patients with relapsing remitting clinical disease. We employed two-color immunostaining and confocal microscopy to identify phenotypes of IL-16-containing cells in frozen tissue sections from MS lesions. RESULTS We found markedly increased levels of pro- and secreted IL-16 (80 kD and 22 kD, respectively) in MS lesions compared to controls. Levels of IL-16 peaked in acute, diminished in subacute, and were elevated again in chronic active lesions. Compared to lesions, lower but still appreciable IL-6 levels were measured in normal-appearing white matter adjacent to active lesions. Levels of IL-16 corresponded to increases in active-caspase-3, T-bet and phosphorylated Stat-1. In MS lesions, we readily observed IL-16 immunoreactivity confined to infiltrating CD3+, T-bet+ and active caspase-3+ mononuclear cells. CONCLUSION We present evidence suggesting that IL-16 production occurs in MS lesions. We show correlations between increased levels of secreted IL-16, CD4+ Th1 cell inflammation, and phosphorylation of axonal cytoskeleton in MS lesions. Overall, the data suggest a possible role for IL-16 in regulation of inflammation and of subsequent changes in the axonal cytoskeleton in MS.
Development and Prospective Validation of a Model for Predicting Weaning in Chronic Ventilator Dependent Patients
(BioMed Central, 2003-11-13) Hendra, Katherine P.; Bonis, Peter A. L.; Joyce-Brady, Martin
BACKGROUND. Approximately ten percent of patients placed on mechanical ventilation during acute illness will require long-term ventilator support. Unfortunately, despite rehabilitation, some will never be liberated from the ventilator. A method of predicting weaning outcomes for these patients could help conserve resources and minimize frustrating failed weaning attempts for this population. The objective of this investigation was to identify predictors of weaning outcome for patients admitted to a chronic ventilator unit (CVU). METHODS. This was a retrospective analysis with prospective validation. The study setting was a 25 bed CVU within a rehabilitation hospital. The training group consisted of 43 patients referred to our facility for weaning after > 3 weeks of mechanical ventilation. A multivariate model to predict weaning outcome was constructed in this group and applied to a prospective group of 31 patients followed during an 18-month period. RESULTS. A modified Glasgow Coma Scale (GCS) and the presence of sustained spontaneous respirations (SSR), defined as the presence of 2 breaths recorded above the ventilator settings on four occasions, were highly predictive of weaning success within six months of CVU admission. Patients with a modified GCS ≥ 8 were 6.5 times more likely to wean than those with a modified GCS < 8 (95% confidence interval 1.6–26.3) and those with SSR were 25.5 times more likely to wean than those without SSR (95% confidence interval 4.3–51.9). CONCLUSIONS. In our population of CVU patients, simple parameters that were available on admission and did not directly reflect cardiopulmonary function were useful predictors of weaning outcome.
Increased frequency and compromised function of T regulatory cells in systemic sclerosis (SSc) Is related to a diminished CD69 and TGFβ expression
(Public Library of Science, 2009-6-22) Radstake, Timothy R. D. J.; Van Bon, Lenny; Broen, Jasper; Wenink, Mark; Santegoets, Kim; Deng, Yanhui; Hussaini, Anila; Simms, Robert; Cruikshank, William W.; Lafyatis, Robert
BACKGROUND. Regulatory T cells (Tregs) are essential in the control of tolerance. Evidence implicates Tregs in human autoimmune conditions. Here we investigated their role in systemic sclerosis (SSc). METHODS/PRINCIPAL FINDINGS. Patients were subdivided as having limited cutaneous SSc (lcSSc, n=20) or diffuse cutaneous SSc (dcSSc, n=48). Further subdivision was made between early dcSSc (n=24) and late dcSSc (n=24) based upon the duration of disease. 26 controls were studied for comparison. CD3+ cells were isolated using FACS and subsequently studied for the expression of CD4, CD8, CD25, FoxP3, CD127, CD62L, GITR, CD69 using flow cytometry. T cell suppression assays were performed using sorted CD4CD25highCD127- and CD4CD25lowCD127high and CD3+ cells. Suppressive function was correlated with CD69 surface expression and TGFβ secretion/expression. The frequency of CD4+CD25+ and CD25highFoxP3highCD127neg T cells was highly increased in all SSc subgroups. Although the expression of CD25 and GITR was comparable between groups, expression of CD62L and CD69 was dramatically lower in SSc patients, which correlated with a diminished suppressive function. Co-incubation of Tregs from healthy donors with plasma from SSc patients fully abrogated suppressive activity. Activation of Tregs from healthy donors or SSc patients with PHA significantly up regulated CD69 expression that could be inhibited by SSc plasma. CONCLUSIONS/SIGNIFICANCE. These results indicate that soluble factors in SSc plasma inhibit Treg function specifically that is associated with altered Treg CD69 and TGFβ expression. These data suggest that a defective Treg function may underlie the immune dysfunction in systemic sclerosis.
Comparison of Proteomic and Transcriptomic Profiles in the Bronchial Airway Epithelium of Current and Never Smokers
(Public Libary of Science, 2009-4-9) Steiling, Katrina; Kadar, Aran Y.; Bergerat, Agnes; Flanigon, James; Sridhar, Sriram; Shah, Vishal; Ahmad, Q. Rushdy; Brody, Jerome S.; Lenburg, Marc E.; Steffen, Martin; Spira, Avrum
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.
On the Analysis of Genome-Wide Association Studies in Family-Based Designs: A Universal, Robust Analysis Approach and an Application to Four Genome-Wide Association Studies
(Public Library of Science, 2009-11-26) Won, Sungho; Wilk, Jemma B.; Mathias, Rasika A.; O'Donnell, Christopher J.; Silverman, Edwin K.; Barnes, Kathleen; O'Connor, George T.; Weiss, Scott T.; Lange, Christoph
For genome-wide association studies in family-based designs, we propose a new, universally applicable approach. The new test statistic exploits all available information about the association, while, by virtue of its design, it maintains the same robustness against population admixture as traditional family-based approaches that are based exclusively on the within-family information. The approach is suitable for the analysis of almost any trait type, e.g. binary, continuous, time-to-onset, multivariate, etc., and combinations of those. We use simulation studies to verify all theoretically derived properties of the approach, estimate its power, and compare it with other standard approaches. We illustrate the practical implications of the new analysis method by an application to a lung-function phenotype, forced expiratory volume in one second (FEV1) in 4 genome-wide association studies. Author Summary In genome-wide association studies, the multiple testing problem and confounding due to population stratification have been intractable issues. Family-based designs have considered only the transmission of genotypes from founder to nonfounder to prevent sensitivity to the population stratification, which leads to the loss of information. Here we propose a novel analysis approach that combines mutually independent FBAT and screening statistics in a robust way. The proposed method is more powerful than any other, while it preserves the complete robustness of family-based association tests, which only achieves much smaller power level. Furthermore, the proposed method is virtually as powerful as population-based approaches/designs, even in the absence of population stratification. By nature of the proposed method, it is always robust as long as FBAT is valid, and the proposed method achieves the optimal efficiency if our linear model for screening test reasonably explains the observed data in terms of covariance structure and population admixture. We illustrate the practical relevance of the approach by an application in 4 genome-wide association studies.
Genetic Variation and Antioxidant Response Gene Expression in the Bronchial Airway Epithelium of Smokers at Risk for Lung Cancer
(Public Library of Science, 2010-8-3) Wang, Xuting; Chorley, Brian N.; Pittman, Gary S.; Kleeberger, Steven R.; Brothers, John; Liu, Gang; Spira, Avrum; Bell, Douglas A.
Prior microarray studies of smokers at high risk for lung cancer have demonstrated that heterogeneity in bronchial airway epithelial cell gene expression response to smoking can serve as an early diagnostic biomarker for lung cancer. As a first step in applying functional genomic analysis to population studies, we have examined the relationship between gene expression variation and genetic variation in a central molecular pathway (NRF2-mediated antioxidant response) associated with smoking exposure and lung cancer. We assessed global gene expression in histologically normal airway epithelial cells obtained at bronchoscopy from smokers who developed lung cancer (SC, n=20), smokers without lung cancer (SNC, n=24), and never smokers (NS, n=8). Functional enrichment analysis showed that the NRF2-mediated, antioxidant response element (ARE)-regulated genes, were significantly lower in SC, when compared with expression levels in SNC. Importantly, we found that the expression of MAFG (a binding partner of NRF2) was correlated with the expression of ARE genes, suggesting MAFG levels may limit target gene induction. Bioinformatically we identified single nucleotide polymorphisms (SNPs) in putative ARE genes and to test the impact of genetic variation, we genotyped these putative regulatory SNPs and other tag SNPs in selected NRF2 pathway genes. Sequencing MAFG locus, we identified 30 novel SNPs and two were associated with either gene expression or lung cancer status among smokers. This work demonstrates an analysis approach that integrates bioinformatics pathway and transcription factor binding site analysis with genotype, gene expression and disease status to identify SNPs that may be associated with individual differences in gene expression and/or cancer status in smokers. These polymorphisms might ultimately contribute to lung cancer risk via their effect on the airway gene expression response to tobacco-smoke exposure.
Transcriptional Analysis of Fracture Healing and the Induction of Embryonic Stem Cell-Related Genes
(Public Library of Science, 2009-5-5) Bais, Manish; McLean, Jody; Sebastiani, Paola; Young, Megan; Wigner, Nathan; Smith, Temple; Kotton, Darrell N.; Einhorn, Thomas A.; Gerstenfeld, Louis C.
Fractures are among the most common human traumas. Fracture healing represents a unique temporarily definable post-natal process in which to study the complex interactions of multiple molecular events that regulate endochondral skeletal tissue formation. Because of the regenerative nature of fracture healing, it is hypothesized that large numbers of post-natal stem cells are recruited and contribute to formation of the multiple cell lineages that contribute to this process. Bayesian modeling was used to generate the temporal profiles of the transcriptome during fracture healing. The temporal relationships between ontologies that are associated with various biologic, metabolic, and regulatory pathways were identified and related to developmental processes associated with skeletogenesis, vasculogenesis, and neurogenesis. The complement of all the expressed BMPs, Wnts, FGFs, and their receptors were related to the subsets of transcription factors that were concurrently expressed during fracture healing. We further defined during fracture healing the temporal patterns of expression for 174 of the 193 genes known to be associated with human genetic skeletal disorders. In order to identify the common regulatory features that might be present in stem cells that are recruited during fracture healing to other types of stem cells, we queried the transcriptome of fracture healing against that seen in embryonic stem cells (ESCs) and mesenchymal stem cells (MSCs). Approximately 300 known genes that are preferentially expressed in ESCs and ~350 of the known genes that are preferentially expressed in MSCs showed induction during fracture healing. Nanog, one of the central epigenetic regulators associated with ESC stem cell maintenance, was shown to be associated in multiple forms or bone repair as well as MSC differentiation. In summary, these data present the first temporal analysis of the transcriptome of an endochondral bone formation process that takes place during fracture healing. They show that neurogenesis as well as vasculogenesis are predominant components of skeletal tissue formation and suggest common pathways are shared between post-natal stem cells and those seen in ESCs.
A Genome-Wide Association Study of Pulmonary Function Measures in the Framingham Heart Study
(Public Library of Science, 2009-3-20) Wilk, Jemma B.; Chen, Ting-hsu; Gottlieb, Daniel J.; Walter, Robert E.; Nagle, Michael W.; Brandler, Brian J.; Myers, Richard H.; Borecki, Ingrid B.; Silverman, Edwin K.; Weiss, Scott T.; O'Connor, George T.
The ratio of forced expiratory volume in one second to forced vital capacity (FEV1/FVC) is a measure used to diagnose airflow obstruction and is highly heritable. We performed a genome-wide association study in 7,691 Framingham Heart Study participants to identify single-nucleotide polymorphisms (SNPs) associated with the FEV1/FVC ratio, analyzed as a percent of the predicted value. Identified SNPs were examined in an independent set of 835 Family Heart Study participants enriched for airflow obstruction. Four SNPs in tight linkage disequilibrium on chromosome 4q31 were associated with the percent predicted FEV1/FVC ratio with p-values of genome-wide significance in the Framingham sample (best p-value = 3.6e-09). One of the four chromosome 4q31 SNPs (rs13147758; p-value 2.3e-08 in Framingham) was genotyped in the Family Heart Study and produced evidence of association with the same phenotype, percent predicted FEV1/FVC (p-value = 2.0e-04). The effect estimates for association in the Framingham and Family Heart studies were in the same direction, with the minor allele (G) associated with higher FEV1/FVC ratio levels. Results from the Family Heart Study demonstrated that the association extended to FEV1 and dichotomous airflow obstruction phenotypes, particularly among smokers. The SNP rs13147758 was associated with the percent predicted FEV1/FVC ratio in independent samples from the Framingham and Family Heart Studies producing a combined p-value of 8.3e-11, and this region of chromosome 4 around 145.68 megabases was associated with COPD in three additional populations reported in the accompanying manuscript. The associated SNPs do not lie within a gene transcript but are near the hedgehog-interacting protein (HHIP) gene and several expressed sequence tags cloned from fetal lung. Though it is unclear what gene or regulatory effect explains the association, the region warrants further investigation. Author Summary Cigarette smoking is the primary risk factor for impaired lung function, yet only 20% of smokers develop chronic obstructive pulmonary disease (COPD). This observation, along with family studies of lung function and COPD, suggests that genetic factors influence susceptibility to cigarette smoke. We examined the relationship between common genetic variants and measures of lung function in a sample of 7,691 participants from the Framingham Heart Study and confirmed our observations in 835 participants from the Family Heart Study selected to include cases of airflow obstruction. We identified a variant on chromosome 4 that was strongly associated with FEV1/FVC in the Framingham Study and confirmed the association in the Family Heart Study. The accompanying manuscript identified the same region to be associated with COPD. Several interesting genes are present in the region that we identified, including a gene (HHIP) interacting with a biological pathway involved in lung development, but it is not yet clear which gene in the region explains the association. Our results identified a region of chromosome 4 that warrants further study to understand the genetic effects influencing lung function.
SIEGE: Smoking Induced Epithelial Gene Expression Database
(Oxford University Press, 2004-12-17) Shah, Vishal; Sridhar, Sriram; Beane, Jennifer; Brody, Jerome S.; Spira, Avrum
The SIEGE (Smoking Induced Epithelial Gene Expression) database is a clinical resource for compiling and analyzing gene expression data from epithelial cells of the human intra-thoracic airway. This database supports a translational research study whose goal is to profile the changes in airway gene expression that are induced by cigarette smoke. RNA is isolated from airway epithelium obtained at bronchoscopy from current-, former- and never-smoker subjects, and hybridized to Affymetrix HG-U133A Genechips, which measure the level of expression of ^∼22500 human transcripts. The microarray data generated along with relevant patient information is uploaded to SIEGE by study administrators using the database's web interface, found at http://pulm.bumc.bu.edu/siegeDB. PERL-coded scripts integrated with SIEGE perform various quality control functions including the processing, filtering and formatting of stored data. The R statistical package is used to import database expression values and execute a number of statistical analyses including t-tests, correlation coefficients and hierarchical clustering. Values from all statistical analyses can be queried through CGI-based tools and web forms found on the 'Search' section of the database website. Query results are embedded with graphical capabilities as well as with links to other databases containing valuable gene resources, including Entrez Gene, GO, Biocarta, GeneCards, dbSNP and the NCBI Map Viewer.
Alterations in gene expression in T1α null lung: a model of deficient alveolar sac development
(BioMed Central, 2006-7-25) Millien, Guetchyn; Spira, Avrum; Hinds, Anne; Wang, Junling; Williams, Mary C.; Ramirez, Maria I.
BACKGROUND. Development of lung alveolar sacs of normal structure and size at late gestation is necessary for the gas exchange process that sustains respiration at birth. Mice lacking the lung differentiation gene T1α [T1α(-/-)] fail to form expanded alveolar sacs, resulting in respiratory failure at birth. Since little is known about the molecular pathways driving alveolar sacculation, we used expression microarrays to identify genes altered in the abnormal lungs and, by inference, may play roles in normal lung morphogenesis. RESULTS. Altered expression of genes related to cell-cell interaction, such as ephrinA3, are observed in T1α(-/-) at E18.5. At term, FosB, Egr1, MPK-1 and Nur77, which can function as negative regulators of the cell-cycle, are down-regulated. This is consistent with the hyperproliferation of peripheral lung cells in term T1α (-/-) lungs reported earlier. Biochemical assays show that neither PCNA nor p21 are altered at E18.5. At term in contrast, PCNA is increased, and p21 is decreased. CONCLUSION. This global analysis has identified a number of candidate genes that are significantly altered in lungs in which sacculation is abnormal. Many genes identified were not previously associated with lung development and may participate in formation of alveolar sacs prenatally.
Toll-Like Receptors: A Family of Pattern-Recognition Receptors in Mammals
(BioMed Central, 2002-07-29) Armant, Myriam A.; Fenton, Matthew J.
Toll-like receptors are a family of pattern-recognition receptors in mammals that can discriminate between chemically diverse classes of microbial products, including bacterial cell-wall components, and that can elicit pathogen-specific cellular immune responses. Toll-like receptors share characteristic features with the interleukin-1 and interleukin-18 cytokine receptors and these receptor classes activate similar signal-transduction pathways. The innate immune system uses a variety of germline-encoded pattern-recognition receptors that recognize conserved microbial structures or pathogen-associated molecular patterns, such as those that occur in the bacterial cell-wall components peptidoglycan and lipopolysaccharide. Recent studies have highlighted the importance of Toll-like receptors (TLRs) as a family of pattern-recognition receptors in mammals that can discriminate between chemically diverse classes of microbial products. First identified on the basis of sequence similarity with the Drosophila protein Toll, TLRs are members of an ancient superfamily of proteins, which includes related proteins in invertebrates and plants. TLRs activate innate immune defense reactions, such as the release of inflammatory cytokines, but increasing evidence supports an additional critical role for TLRs in orchestrating the development of adaptive immune responses. The sequence similarity between the intracellular domains of the TLRs and the mammalian interleukin-1 and interleukin-18 cytokine receptors reflects the use of a common intracellular signal-transduction cascade triggered by these receptor classes. But more recent findings have demonstrated that there are in fact TLR-specific signaling pathways and cellular responses. Thus, TLRs function as sentinels of the mammalian immune system that can discriminate between diverse pathogen-associated molecular patterns and then elicit pathogen-specific cellular immune responses.
Reversible and Permanent Effects of Tobacco Smoke Exposure on Airway Epithelial Gene Expression
(BioMed Central, 2007-09-25) Beane, Jennifer; Sebastiani, Paola; Liu, Gang; Brody, Jerome S.; Lenburg, Marc E.; Spira, Avrum
Oligonucleotide microarray analysis revealed 175 genes that are differentially expressed in large airway epithelial cells of people who currently smoke compared with those who never smoked, with 28 classified as irreversible, 6 as slowly reversible, and 139 as rapidly reversible. BACKGROUND. Tobacco use remains the leading preventable cause of death in the US. The risk of dying from smoking-related diseases remains elevated for former smokers years after quitting. The identification of irreversible effects of tobacco smoke on airway gene expression may provide insights into the causes of this elevated risk. RESULTS. Using oligonucleotide microarrays, we measured gene expression in large airway epithelial cells obtained via bronchoscopy from never, current, and former smokers (n = 104). Linear models identified 175 genes differentially expressed between current and never smokers, and classified these as irreversible (n = 28), slowly reversible (n = 6), or rapidly reversible (n = 139) based on their expression in former smokers. A greater percentage of irreversible and slowly reversible genes were down-regulated by smoking, suggesting possible mechanisms for persistent changes, such as allelic loss at 16q13. Similarities with airway epithelium gene expression changes caused by other environmental exposures suggest that common mechanisms are involved in the response to tobacco smoke. Finally, using irreversible genes, we built a biomarker of ever exposure to tobacco smoke capable of classifying an independent set of former and current smokers with 81% and 100% accuracy, respectively. CONCLUSION. We have categorized smoking-related changes in airway gene expression by their degree of reversibility upon smoking cessation. Our findings provide insights into the mechanisms leading to reversible and persistent effects of tobacco smoke that may explain former smokers increased risk for developing tobacco-induced lung disease and provide novel targets for chemoprophylaxis. Airway gene expression may also serve as a sensitive biomarker to identify individuals with past exposure to tobacco smoke.
Environmental and genetic risk factors and gene-environment interactions in the pathogenesis of chronic obstructive lung disease
(National Institute of Environmental Health Sciences, 2000-08) Walter, R.; Gottlieb, D.J.; O'Connor, G.T.
Current understanding of the pathogenesis of chronic obstructive pulmonary disease (COPD), a source of substantial morbidity and mortality in the United States, suggests that chronic inflammation leads to the airways obstruction and parenchymal destruction that characterize this condition. Environmental factors, especially tobacco smoke exposure, are known to accelerate longitudinal decline of lung function, and there is substantial evidence that upregulation of inflammatory pathways plays a vital role in this process. Genetic regulation of both inflammatory responses and anti-inflammatory protective mechanisms likely underlies the heritability of COPD observed in family studies. In alpha-1 protease inhibitor deficiency, the only genetic disorder known to cause COPD, lack of inhibition of elastase activity, results in the parenchymal destruction of emphysema. Other genetic polymorphisms have been hypothesized to alter the risk of COPD but have not been established as causes of this condition. It is likely that multiple genetic factors interacting with each other and with a number of environmental agents will be found to result in the development of COPD.
Cockroach Allergy and Asthma in a 30-Year-Old Man
(National Institute of Environmental Health Sciences, 1999-03) O'Connor, G.T.; Gold, D.R.
A growing body of evidence has implicated allergens derived from cockroaches as an important environmental factor that may aggravate asthma in sensitized persons. We present the case of a 30-year-old man with asthma and a cockroach allergy. Allergy skin testing confirmed hypersensitivity to cockroach extract, and a home visit revealed visual evidence of infestation and the presence of Bla g 1 German cockroach allergen in vacuumed dust. As is typical of patients with a cockroach allergy and asthma, multiple factors in addition to cockroach allergen appeared to aggravate the patient's asthma. A multimodality therapeutic regimen, which included medications as well as cleaning of the home, integrated pest management, and professional application of chemical controls, resulted in substantial clinical improvement. The pathophysiology, epidemiology, and clinical features of cockroach-allergic asthma are reviewed, and an approach to diagnosis and management is suggested.
Standardization and performance evaluation of mononuclear cell cytokine secretion assays in a multicenter study
(BioMed Central, 2006-12-12) Shreffler, Wayne G.; Visness, Cynthia M.; Burger, Melissa; Cruikshank, William W.; Lederman, Howard M.; de la Morena, Maite; Grindle, Kristine; Calatroni, Agustin; Sampson, Hugh A.; Gern, James E.
BACKGROUND: Cryopreservation of peripheral blood mononuclear cells has been used to preserve and standardize immunologic measurements for multicenter studies, however, effects of cryopreservation on cytokine responses are incompletely understood. In designing immunologic studies for a new multicenter birth cohort study of childhood asthma, we performed a series of experiments to determine the effects of two different methods of cryopreservation on the cytokine responses of cord and peripheral blood mononuclear cells. RESULTS: Paired samples of PBMC were processed freshly, or after cryopreservation in a Nalgene container (NC) or a controlled-rate freezer (CRF). Although there were some differences between the methods, cryopreservation inhibited PHA-induced IL-10 secretion and Der f 1-induced IL-2 secretion, and augmented PHA-induced IL-2 secretion and spontaneous secretion of TNF-α. In separate experiments, NC cryopreservation inhibited secretion of several cytokines (IL-13, IL-10, IFN-γ, TNF-α) by PHA-stimulated cord blood mononuclear cells. With the exception of PHA-induced IL-13, results from fresh and cryopreserved cord blood samples were not significantly correlated. Finally, in reproducibility studies involving processing of identical cell samples in up to 4 separate laboratories, variances in cytokine responses of fresh cells stimulated at separate sites did not exceed those in cryopreserved cells stimulated at a central site. CONCLUSION: Collectively, these studies indicate that cryopreservation can affect mononuclear cell cytokine response profiles, and that IL-10 secretion and antigen-induced responses may be especially vulnerable. These studies also demonstrate that mononuclear cell responses can be standardized for performance in a small number of laboratories for multicenter studies, and underscore the importance of measuring reproducibility and of testing whether cryopreservation techniques alter specific immunologic outcomes.

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