The mechanisms by which epithelial progenitor cells integrate local signals to balance proliferation with differentiation and regulate patterning during lung organogenesis are still poorly understood. The Hippo pathway and its transcription co-activator Yap have recently emerged as major regulators of progenitor cell expansion and differentiation in development and cancer. Here we investigated the role of Yap signaling in the cellular and molecular events associated with lung epithelial morphogenesis and differentiation. We provide evidence that when airway epithelial tubules are forming and branching, a nuclear to cytoplasmic shift of Yap marks the boundary between the progenitors of the distal lung and the airway compartment. At this transition zone, Yap specifies a transcriptional program that controls the expression of Sox2, restricting distal gene expression and initiating an airway progenitor cell program key to generate the airway epithelium and its branched tubular structures. In Yap deficient mice, epithelial progenitors are unable to properly respond to local Tgf beta-induced cues to control levels and distribution of Sox2, resulting in expansion of the distal epithelial compartment and inability to form airways. Moreover, we show that Yap levels and phosphorylation status play a major role in regulating differentiation of airway progenitors later in development and in adult life. Analysis of YAP-interacting partners in adult airway progenitors by Mass Spectroscopy suggests phosphorylated Yap interactions with ciliome proteins. Our study reveals a crucial role for Yap in specification and differentiation of airway progenitors likely to be also relevant in regeneration-repair of the adult airway epithelium.

EXPOSITION PENDANT LA GESTATION A DES NANOPARTICULES MANUFACTUREES : IMPACT SUR LE DEVELOPPEMENT PULMONAIRE DE LA DESCENDANCELe développement de l’utilisation des nanoparticules (NP) comme les NP d’argent (Ag), de dioxyde de titane (TiO2) et de dioxyde cérium (CeO2) conduit à s’intéresser à leurs potentiels effets toxiques. Des travaux ont montré que l’exposition de souris par voie pulmonaire aux NP peut induire une réponse inflammatoire et la fibrose pulmonaire. En revanche, il existe très peu de données concernant l’impact de l’exposition à des NP sur la descendance. Le but de cette étude est d’évaluer les conséquences d’une exposition de souris à des NP par voie respiratoire sur le développement pulmonaire de la descendance, ainsi que de déterminer le mécanisme d’action induisant les altérations du développement pulmonaire. Pour cela, trois NP de même taille et forme ont été utilisées : TiO2, Ag, et CeO2, afin d’évaluer l’impact des propriétés physico-chimiques des NP sur le développement pulmonaire. Des souris femelles gestantes ont été exposées aux NP par voie pulmonaire une fois par semaine. Des analyses pulmonaires de la descendance ont été réalisées à différentes étapes du développement pulmonaire, avant (17,5 jours post-coït) et après la naissance (14,5 et 49,5 jours post-délivrance). Les résultats montrent qu’après exposition pulmonaire pendant la gestation, les NP induisent une altération de développement pulmonaire de la descendance quelle que soit la nature de la NP utilisée. Ces résultats étaient accompagnés d’une diminution de l’efficacité placentaire associée à la présence des NP dans le placenta et à la diminution de l’expression de VEGF-alpha et MMP-9 à l’âge foetal, et FGF-18 au stage de l’alvéolisation pulmonaire. Compte tenu de l’utilisation croissante de NP, ces résultats suscitent des inquiétudes quant à la santé de l’Homme en particulier en cas d’exposition des femmes enceintes, dont le foetus en développement est susceptible d’avoir un retentissement pulmonaire de l’exposition à ces NP.Mots-clés : nanoparticules, gestation, développement pulmonaire / EXPOSURE TO MANUFACTURED NANOPARTICLES DURING GESTATION: IMPACT ON THE RESPIRATORY TRACT OF THE OFFSPRINGDue to several commercial applications of nanoparticles (NPs), such as silver (Ag), titanium dioxide (TiO2) and cerium dioxide (CeO2), knowledge of the toxicity of those NPs is of great importance. It has been shown that exposure to NPs may lead to an inflammatory response and pulmonary fibrosis. However less is known on the effect of exposure to NPs on the offspring. Therefore the aim of this study is to assess the impact of exposure by the respiratory route to various NPs during pregnancy on lung development of the offspring, and to determine the key parameters involved in lung alterations. We used three NPs: TiO2, Ag, and CeO2, to assess the impact of NPs physico-chemical properties on the potential effects on lung development. Pregnant mice were exposed weekly to 100 μg NPs or saline by nonsurgical intratracheal instillation. Analysis of the lungs of the offspring was performed at different times of lung development, before (17.5 gestational day) and after birth (14.5 and 49.5 post-delivery day). Results showed that after pulmonary exposure during pregnancy, all nanoparticles induced a long-lasting impairment of lung development of the offspring. This was accompanied by a decreased placental efficiency which was associated with the presence of NP in placenta and a decreased pulmonary expression of VEGF-alpha and MMP-9 at the fetal stage, and FGF-18 at the alveolization stage. In view of the growing use of these nanoparticles, this result raise concerns for public health and pregnant women and their developing fetus particularly for those at high risk of occupational or domestic exposure.Keywords: nanoparticles, pregnancy, lung development

Of the 800,000 suicides recorded globally every year, over a third are due to pesticide ingestion, the majority of which occur in rural Asia with organophosphorus (OP) compounds. These anticholinesterase pesticides cause an acute cholinergic syndrome characterised by decreased consciousness, excessive airway secretions and respiratory failure. A combination of these clinical features is the most common cause of death. Up to 30% of OP pesticide poisoned patients are admitted to the Intensive Care Unit (ICU) for tracheal intubation and lung ventilation, but up to half die. It is not understood why the case fatality for intubated poisoned patients is so high, but one hypothesis is that the patients, when unconscious, aspirate their stomach contents (including the OP and the solvent present in its agricultural formulation) causing a toxic lung injury which contributes to the observed high mortality. In this PhD, I aimed to characterise the lung injury caused by OP pesticide self-poisoning through both indirect (ingestion) and direct (aspiration) means. To achieve this, I analysed data from previous toxicological minipig work and designed and conducted a specific minipig pulmonary aspiration study which was complemented by an experimental OP poisoning ex vivo lung perfusion model and human data from pesticide poisoned patients in Sri Lanka. I first investigated the pulmonary pathophysiology resulting from orogastric administration of OP pesticide without aspiration. Analysis of my group’s Gottingen minipig in vivo work demonstrated that orogastric placement of agricultural OP (dimethoate EC40) produced lung injury via exposure to blood-borne pesticide. Pathological lung changes consisted of alveolar and interstitial oedema, pulmonary haemorrhage and modest neutrophilia with increased concentrations of protein, IL-6 and IL-8 when compared with controls, but with low concentrations of TNF-α and IL-10 in bronchoalveolar lavage fluid (BALF). In a second study, OP poisoned minipigs had increased concentrations of BALF protein, neutrophils, IL-8 and CRP six hours after orogastric poisoning when compared with their baseline values. Electron microscopy images of both studies demonstrated damage to the alveolar capillary membrane secondary to systemic OP poisoning. Prior to conducting the main pulmonary aspiration study in minipigs, there was considerable refinement of the processes involved through use of: (i) pilot aspiration and dose ranging studies; (ii) the development of a specific pulmonary histopathological scoring system; and (iii) employment of modern human anaesthetic equipment and intensive care patient management protocols. After this period of model development, an in vivo 48 hour study using Gottingen minipigs (n=26) was conducted to investigate the pulmonary pathophysiology in animals given either sham bronchoscopy (sham control) or 0.5 mL/kg of: saline (saline control), porcine gastric juice [GJ], OP (dimethoate EC40) + GJ [OP+GJ], or solvent (cyclohexanone) + GJ [Solv+GJ] into the right lung under bronchoscopic guidance. The results showed that in a minipig model OP and GJ placed into one lung created a direct (right) and indirect (left) lung injury significantly different to controls, and in some respects worse than GJ alone 48 hours after poisoning. The direct lung injury caused by OP+GJ was characterised by significantly worse pathology (p=0.0003) in terms of: pulmonary neutrophilia, alveolar haemorrhage, necrosis, oedema and fibrin deposition, when compared with sham controls at 48 hours. Lungs injured directly with OP+GJ also had significantly higher concentrations of BALF neutrophils (p≤0.01), protein (p≤0.05), IL-6 (p≤0.01), IL-8 (p≤0.01) and CRP (p≤0.05) at 24 hours, and BALF protein (p≤ 0.01), and CRP (p≤ 0.05) when compared with sham controls at 48 hours. The BALF from OP+GJ minipigs at 48 hours also had higher numbers of aerobic bacteria than other groups, suggesting the development of pneumonia could be a source of additional lung injury. Lung damage might also have resulted from a reduction in the surfactant component responsible for the lowering of alveolar surface tension. Direct lung injury with OP+GJ caused a proportional reduction of beneficial pulmonary surfactant phosphatidylcholine (PC) species 16:0/16:0 [29(±4) % vs. 38(±4) %] when compared with sham controls at 48 hours. Unlike the other groups, OP+GJ (direct and indirectly-injured) lungs had type 2 alveolar cell ultrastructural morphological differences in the lamellar bodies that stored the surfactant. The lamellar bodies were more numerous and more dense in the OP+GJ lungs compared with other groups and could signify a failure of surfactant release or some other pathology pertinent to OP aspiration lung injury. Computed tomography analysis showed that direct lung injury with OP+GJ caused significantly more lung tissue to be poorly or non-aerated [77 (±13) % ; p≤0.0001 when compared with sham] as opposed to 62 (±27) % in GJ, 53(±13)% in sham and 47(±0.2)% in saline control animals by 47.5 hours and was mainly due to pulmonary haemorrhage and oedema fluid. The key differences between aspiration of OP+GJ versus GJ alone was that the majority of inflammatory markers (e.g. BALF protein, IL-6 and CRP) appeared to increase from 24-48 hours in OP+GJ treated animals, but decreased in GJ pigs, possibly signifying resolution. Treatment with GJ alone produced less severe histopathological damage, bacterial BALF numbers and percentage of poorly and non-aerated lung tissue. Importantly, there was less evidence of indirect lung injury within the GJ pigs when compared with animals treated with OP+GJ. Solvent placed into the lung seemed to offer some form of protection from the effects of GJ aspiration. This was dramatically demonstrated by the histopathology scores, proportional percentage of beneficial phosphatidylcholine (PC) species 16:0/16:0 and the percentage of poorly and non-aerated lung tissue all approaching control animal levels by 48 hours in minipigs that had Solv+GJ placed in the directly-injured (right) lung. Further evidence of benefit was provided by statistically significant reductions (p≤ 0.05) in BALF concentrations of IL-8, IL-6 and CRP in minipigs which had aspirated Solv+GJ when compared with OP+GJ and/or GJ minipig groups at 24 hours. The pathophysiology of aspirated OP+GJ was also investigated in a pilot ovine ex vivo lung perfusion (EVLP) model (n=4). Lungs directly-injured with OP+GJ had higher concentrations of total protein (4300 mg/L vs. 350 mg/L) with a proportional reduction of beneficial pulmonary surfactant phosphatidylcholine species 16:0/16:0 (27% vs.34%) when compared with control lungs. Analysis of toll-like receptor (TLR) lung tissue expression in the OP+GJ directly and indirectly-injured lungs indicated that inflammatory mechanisms might also involve upregulation of TLR 3 and 5, unlike other lung injuries e.g. those induced with lipopolysaccharide, which typically upregulates TLR 2 and 4. To compare OP-induced lung injury in humans and the minipigs, a small feasibility study was conducted in the ICUs of the University of Peradeniya hospital, Sri Lanka. Unfortunately, ethics review and recruitment proved more difficult than expected and we failed to recruit to target. We did however find raised BALF concentrations of IL-6, IL-8 and CRP and low concentrations of TNF, IL-1β, IL-10 in intubated OP poisoned patients at 24 hours when compared with controls. We also found that two plasma micro-RNA biomarkers thought to be involved in inflammation and lung injury, MiR-21 and MiR-146a, had significantly reduced expression in OP-poisoned patients with aspiration compared to non-intubated control patients from the UK (p=0.008 and p=0.0083 respectively). The work from this thesis has allowed the characterisation of both indirect and direct lung injuries caused by OP pesticide ingestion and aspiration. The minipig model showed that at 48 hours the lung injury created by aspiration of OP+GJ appeared more severe than GJ alone, but the addition of the solvent cyclohexanone seemed protective and even beneficial in the context of GJ aspiration. The cytokine expression profiles from both the human and minipig work, combined with the preliminary TLR lung tissue analysis from the EVLP model, suggest that OP+GJ aspiration is unlike normal GJ aspiration and classic ARDS. / Increased concentrations of aerobic bacteria in the minipig OP+GJ lungs at 48 hours and evidence of suppression of plasma miR-21 and miR-146a in OP poisoned patients could be linked, and may involve cholinergic immune system modulation. These molecular mechanisms need to be investigated further in both in vitro and in vivo models. These discoveries indicate the complex nature of the pulmonary injury that occurs after OP pesticide poisoning, and suggests that damage is not caused by gastric contents alone. Preliminary findings indicate that aspiration of OP+GJ could create favourable conditions for the development of aspiration or ventilator-associated pneumonia but this would need confirmation in larger clinical studies. The potential roles of micro RNA as a biomarker of OP poisoning and lung injury, and solvent as a therapy for aspiration should be explored in further pre-clinical studies.

Lung cancer has developed from a rare condition into the leading cause of cancerrelated death in the United Kingdom. Lung cancer patients face a disease with a high symptom burden, increased psychosocial needs and a high mortality. Supportive care needs are often relevant from diagnosis. Despite this there are no clear follow-up structures for lung cancer patients that address both cancer management and supportive care. The aims of this study were to evaluate supportive care needs, assess predictors of such needs and identify factors which could aid service provision within Stobhill lung cancer services. Methods Supportive care needs were measured using an adapted Palliative Outcome Scale (POS), incorporated within a larger questionnaire. All lung cancer patients attending the clinic could complete this questionnaire. Respiratory symptoms, performance status, service usage, preferences and satisfaction were also assessed. Data were stratified to allow evaluation of three clinical groupings: all patients, newly diagnosed patients and patients in the last three months of life. Analyses were phased: descriptive analyses, univariate tests of association and multivariate regression. Results Three hundred and fifty three lung cancer patients completed questionnaires. The high symptom burden in lung cancer was confirmed. Anxiety, pain and dyspnoea were identified as the key issues. Poor performance status was identified to be an independent predictor of increased POS score, increased anxiety, increased pain and increased dyspnoea. There was no independent relationship between POS and survival. Although the majority of patients were satisfied with the care received, there was uncertainty regarding who was in charge of care and some disparity in preferred structure for follow-up. Conclusions Despite recent advances in lung cancer management, improvements are still required to address unmet supportive care needs of patients. Particular attention should be given to those with poorer performance status to effectively identify and meet such needs.

Thesis (M.A.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / Cigarette smoke creates a molecular field of injury in epithelial cells that line the respiratory tract. We hypothesized that transcriptome sequencing (RNA-seq) will enhance our understanding of the field of molecular injury in response to tobacco smoke exposure and lung cancer pathogenesis by identifying gene expression differences not interrogated or accurately measured by microarrays. We sequenced the high- molecular weight fraction of total RNA (>200 nt) from pooled bronchial airway epithelial cell brushings (n = 3 patients per pool) obtained during bronchoscopy from healthy never smoker (NS) and current smoker (S) volunteers and smokers with (C) and without ( C) lung cancer undergoing lung nodule resection surgery. RNA-seq libraries were prepared using two distinct approaches, one capable of capturing non-polyadenylated RNA (the prototype NuGEN Ovation RNA-seq protocol) and the other designed to measure only polyadenylated RNA (the standard Illumina mRNA-seq protocol) followed by sequencing generating approximately 29 million 36 nt reads per pool and approximately 22 million 75 nt paired-end reads per pool, respectively. The NuGEN protocol captured additional transcripts not detected by the Illumina protocol at the expense of reduced coverage of polyadenylated transcripts, while longer read lengths and a paired-end sequencing strategy significantly improved the number of reads that could be aligned to the genome. The aligned reads derived from the two complementary protocols were used to define the compendium of genes expressed in the airway epithelium (n = 20,573 genes). Pathways related to the metabolism of xenobiotics by cytochrome P450, retinol metabolism, and oxidoreductase activity were enriched among genes differentially expressed in smokers, whereas chemokine signaling pathways, cytokine-cytokine receptor interactions, and cell adhesion molecules were enriched among genes differentially expressed in smokers with lung cancer. There was a significant correlation between the RNA-seq gene expression data and Affymetrix microarray data generated from the same samples (P < 0.001); however, the RNA-seq data detected additional smoking- and cancer-related transcripts whose expression was were either not interrogated by or was not found to be significantly altered when using microarrays, including smoking- related changes in the inflammatory genes SIOOA8 and SIOOA9 and cancer-related changes in MUC5AC and secretoglobin (SCGB3Al). Quantitative realtime PCR confirmed differential expression of select genes and non-coding RNAs within individual samples. These results demonstrate that transcriptome sequencing has the potential to provide new insights into the biology of the airway field of injury associated with smoking and lung cancer. The measurement of both coding and non-coding transcripts by RNA-seq has the potential to help elucidate mechanisms of response to tobacco smoke and to identify additional biomarkers of lung cancer risk and novel targets for chemoprevention. / 2031-01-01

The respiratory system forms a major mucosal interface with the external environment. Consequently, the respiratory tract is constantly exposed to inhaled foreign antigens, commensal microorganisms, and potential pathogens. The respiratory system has evolved a complex regulatory network designed to prevent unnecessary inflammation to harmless antigens and to limit immune-mediated damage to the fragile lung epithelium in response to infection. The lung maintains a default anti-inflammatory state that is coordinated by the respiratory epithelium, alveolar macrophages, dendritic cells, and regulatory Foxp3+ CD4 T cells (Tregs). It is likely that all of these cells influence the development of pathogen-specific T cell responses in the lung. Following infection with a respiratory virus, virus-specific CD8 T cells in the lung are inhibited in their ability to produce cytokines. Current studies suggest that this functional inactivation occurs following infection with respiratory viruses within the Paramyxoviridae family. The data presented here demonstrate that suppression of effector functions of virus-specific CD8 T cells in the lungs occurs following infection with several unrelated respiratory viruses. These results indicate that the functional inhibition of virus-specific T cell responses is not restricted to infection with viruses from the Paramyxoviridae family. Furthermore, I show data indicating that the functional inactivation of virus-specific CD8 T cells in the lungs occurs in the absence of infection. I also demonstrate for the first time that the lung environment also regulates the effector functions of virus-specific CD4 T cells. Inhibition of cytokine production by pulmonary T cells is reversible as stimulation with exogenous peptide-pulsed antigen-presenting cells rescues IFN-gamma production. The inhibition of IFN-gamma production by virus-specific T cells occurs in other organs such as the kidney. These data suggest that regulation of T cell cytokine production by peripheral tissues may serve as an important mechanism to prevent immunopathology and preserve normal tissue function. Foxp3+ Tregs have been shown to inhibit conventional effector T cell responses in a large number of chronic infection models. However, their role during acute infections remains unclear. Examination of Foxp3+ Tregs during RSV infection showed that Tregs are rapidly recruited into the lungs and acquire an activated phenotype. Depletion of Foxp3+ Tregs prior to RSV infection revealed that Tregs facilitate the early recruitment of RSV-specific CD8 T cells from the draining lymph nodes to the lung and later limit the overall magnitude of the virus-specific CD8 T cell response. Depletion of Tregs increased TNF-αa production by RSV-specific CD8 T cells and enhanced T-cell-mediated immunopathology. These data demonstrate that Foxp3+ Tregs play a major role in regulating CD8 T cell responses to respiratory virus infections. Collectively, the data presented here demonstrate that CD8 T cell responses to respiratory pathogens are tightly regulated within the lung environment.

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This thesis reports on our initial work constructing a human lung query atlas which provides clinically relevant population statistics for normal and abnormal individuals. The atlas incorporates front-end interfaces with back-end database. The interfaces were developed using Microsoft Access 2007 and the database was implemented using MySQL. ODBC was used to import database into Access and provide connection for database and interfaces. VBA is used to write SQL queries and realized the interaction with interfaces. SQL queries is written to extract the data which researchers may interest in. The atlas provides measurements of the human airway tree and lung volumes from a population of individuals and also provides a population statistics based on age, race, ethnicity, gender and other information. It also provides functionality for comparing airway measurements between populations, individuals to a population, and individuals to individuals. Statistical significance, such as p-value, is provided to analyze two individuals or populations.