Chronic Obstructive Pulmonary Disease (COPD) is a progressive respiratory disease characterized by airway inflammation and abnormal alveolar enlargement. It is the third leading cause of death around the world. Although extensive research efforts have been made, there is still no curable treatment available for lung tissue damage in patients with COPD. Therefore, it is of great significance to elucidate the mechanisms of tissue damage and repair in COPD. As the first barrier against environmental insults and pathogens, pulmonary epithelial cells play an essential role in regulating injury response and repair. However, how pulmonary epithelial cells contribute to irreversible alveolar destruction in COPD is not well understood. In this study, we elucidated the mechanisms of epithelial cell damage in both cigarette smoke-induced COPD and alpha1 antitrypsin deficiency (AATD)-associated genetic COPD. To investigate alveolar epithelial cell damage and repair in cigarette smoke-induced emphysema, a lineage tracing model was utilized to fluorescently label and chase alveolar type II (AT2) epithelial cells, the adult progenitor cells in the alveolar epithelium. An assessment of cigarette smoke-induced changes in cellular composition and regenerative capacity of the alveolar epithelial cells was performed. Cigarette smoke was found to impede the AT2-directed alveolar epithelial regeneration and repair process, and this impaired progenitor cell function was not restored after smoke cessation. Moreover, comparison analysis between stains that are sensitive and resistant to smoke-induced damage revealed that deficiency in lipid metabolism may contribute to the dysregulation of alveolar epithelial repair by AT2 cells. Restoring alveolar progenitor functions through lipid metabolism may serve as a novel therapeutic for alveolar destruction in smoke-induced COPD. To explore the mechanism of epithelial damage in AATD-associated genetic COPD, we utilized a PiZ (p.Glu342Lys) transgenic mouse model expressing human ZAAT protein. Morphometric analysis of PiZ lungs suggests that the accumulation of ZAAT polymers in the lung directly leads to the spontaneous development of emphysema. To investigate epithelial damage induced by zAAT accumulation, we isolated the epithelial cell population from the lung of PiZ mice. We identified epithelial-specific expression of cleaved caspase 3, indicating a direct cytotoxic effect of ZAAT in impairing epithelial function and inducing epithelial cell death. Future therapeutics could directly target the cytotoxicity of pulmonary epithelial cells in AATD to reduce lung tissue damage. Overall, our findings suggest that pulmonary epithelial damage plays an essential role in the pathogenesis of lung tissue damage in COPD. Future epithelial cell-based therapies may contribute to pulmonary re-epithelialization and tissue repair in both cigarette smoke-induced and AATD-associated COPD.

Chan, Wai Kiu. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 233-256). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract and appendix also in Chinese.

Chronic obstructive pulmonary disease (COPD) and emphysema together are one of the leading causes of death in the United States and worldwide; meanwhile, breast cancer has the highest incidence and second-highest mortality burden of all cancers in women. Imaging markers relevant to each of these conditions are readily identifiable on chest computed tomography (CT): (1) visually-appreciable variants in airway tree structure exist which are associated with increased odds for development of COPD; (2) CT emphysema subtypes (CTES), based on lung texture and spatial features, have been identified by unsupervised clustering and correlate with functional measures and clinical outcomes; (3) dysanapsis, or the ratio of airway caliber to lung volume, is the strongest known predictor of COPD risk, and (4) breast density (i.e., the extent of fibroglandular tissue within the breast) is strongly associated with breast cancer risk. Machine- and deep-learning frameworks present an opportunity to address unmet needs in each of these directions, leveraging the data from large CT cohorts. Application of unsupervised learning approaches serves to discover new, image-based phenotypes. While topologic and geometric variation in the structure of the CT-resolved airway tree are well-described, tree- structural subtypes are not fully characterized. Similarly, while the clinical correlates of CTES have been described in large cohort studies, the association of CTES with structural and functional measures of the lung parenchyma are only partially described, and the time-dependent evolution of emphysematous lung texture has not been studied. Supervised approaches are required to automate CT image assessment, or to estimate CT- based measures from incomplete input data. While dysanapsis can be directly quantified on full- lung CT, the lungs are often only partially imaged in large CT datasets; total lung volume must then be regressed from the observed partial image. Breast density grades, meanwhile, are generally visually assessed, which is laborious to perform at scale. Moreover, current automated methods rely on segmentation followed by intensity thresholding, excluding higher-order features which may contribute to the radiologist assessment. In this thesis, we present a series of machine-learning methods which address each of these gaps in the field, using CT scans from the Multi-Ethnic Study of Atherosclerosis (MESA), the SubPopulations and InteRmediate Outcome Measures in COPD (SPIROMICS) Study, and an institutional chest CT dataset acquired at Columbia University Irving Medical Center. First, we design a novel graph-based clustering framework for identifying tree-structure subtypes in Billera-Holmes-Vogtmann (BHV) tree-space, using the airway trees segmented from the full-lung CT scans of MESA Lung Exam 5. We characterize the behavior of our clustering algorithm on a synthetic dataset, describe the geometric and topological variation across tree-structure clusters, and demonstrate the algorithm’s robustness to perturbation of the input dataset and graph tuning parameter. Second, in MESA Lung Exam 5 CT scans, we quantify the loss of small-diameter airway and pulmonary vessel branches within CTES-labeled lung tissue, demonstrating that depletion of these structures is concentrated within CTES regions, and that the magnitude of this effect is CTES-specific. In a sample of 278 SPIROMICS Visit 1 participants, we find that CTES demonstrate distinct patterns of gas trapping and functional small airways disease (fSAD) on expiratory CT imaging. In the CT scans of SPIROMICS participants imaged at Visit 1 and Visit 5, we update the CTES clustering pipeline to identify longitudinal emphysema patterns (LEPs), which refine CTES by defining subphenotypes informative of time-dependent texture change. Third, we develop a multi-view convolutional neural network (CNN) model to estimate total lung volume (TLV) from cardiac CT scans and lung masks in MESA Lung Exam 5. We demonstrate that our model outperforms regression on imaged lung volume, and is robust to same- day repeated imaging and longitudinal follow-up within MESA. Our model is directly applicable to multiple large-scale cohorts containing cardiac CT and totaling over ten thousand participants. Finally, we design a 3-D CNN model for end-to-end automated breast density assessment on chest CT, trained and evaluated on an institutional chest CT dataset of patients imaged at Columbia University Irving Medical Center. We incorporate ordinal regression frameworks for density grade prediction which outperform binary or multi-class classification objectives, and we demonstrate that model performance on identifying high breast density is comparable to the inter-rater reliability of expert radiologists on this task.

Lau Yin Kei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 58-79). / Abstracts in English and Chinese. / Acknowledgement --- p.I / Abstract --- p.IV / Abstract in Chinese --- p.VI / Abbreviations --- p.VIII / Introduction --- p.1 / Chapter 1.1 --- Prevalence of COPD and asthma in Hong Kong --- p.1 / Chapter 1.2 --- Players in pathogenesis of COPD --- p.2 / Chapter 1.3 --- Players in pathogenesis of asthma --- p.4 / Chapter 1.4 --- The use of exhaled breath condensate in previous studies --- p.6 / Chapter 1. 5 --- Brief overview of chemokines --- p.8 / Chapter 1.6 --- Objective of this study --- p.12 / Materials and methods --- p.14 / Chapter 2.1 --- Study population --- p.14 / Chapter 2.1.1 --- Patients with COPD and control subjects --- p.14 / Chapter 2.1.2 --- Patients with asthma and control subjects --- p.15 / Chapter 2.2 --- Lung function --- p.15 / Chapter 2.3 --- Dyspnoea score measurement of patients with COPD --- p.16 / Chapter 2.4 --- Classification of patients and asthma severity --- p.16 / Chapter 2.5 --- Skin prick test and blood tests --- p.16 / Chapter 2.6 --- Collection of exhaled breath condensate --- p.17 / Chapter 2.7 --- Measurement of constituent in EBC --- p.17 / Chapter 2.7.1 --- "Measurement of 8-isoprostane, MCP-1 and GROα in patients with COPD and the corresponding control subjects" --- p.17 / Chapter 2.7.2 --- Measurement of eotaxin and MDC of patients with asthma and the corresponding control subjects --- p.18 / Chapter 2.8 --- Reproducibility of exhaled breath constituent --- p.18 / Chapter 2.8.1 --- "Assessment of reproducibility of the exhaled MCP-1, GROα and8- isoprostane measurements" --- p.19 / Chapter 2.8.2 --- Assessment of reproducibility of the exhaled eotaxin and MDC measurement --- p.19 / Chapter 2.9 --- Statistical analysis --- p.19 / Results --- p.21 / Chapter 3.1 --- Patients with COPD and corresponding control subjects --- p.21 / Chapter 3.2 --- Patients with asthma and corresponding control subjects --- p.28 / Discussion --- p.36 / Chapter 4.1 --- "Exhaled 8-isoprostane, GRO-α and MCP-1 of patients with COPD and corresponding control subjects" --- p.36 / Chapter 4.2 --- Exhaled eotaxin and MDC from patients with asthma and corresponding control subjects --- p.43 / Chapter 4.3 --- Technical aspects of EBC assessment --- p.49 / Future prospect --- p.54 / Conclusion --- p.56 / References --- p.58 / Tables and Figures / Table 1. Demographics of the COPD and control subjects --- p.22 / Figure 1. The level of 8-isoprostane in the exhaled breath condensate of COPD and control subjects --- p.23 / Figure 2. The level of GROa in the exhaled breath condensate of COPD and control subjects --- p.25 / "Figure 3 Bland and Altman's Plot of the repeatability of 8-isoprostane, GROa and MCP-1 in the exhaled breath condensate of normal controls" --- p.27 / Table2. Clinical and physiological details of the subjects --- p.29 / Figure 4. Level of eotaxin in exhaled breath condensate of asthma and control subjects --- p.30 / Figure 5 Level of MDC in exhaled breath condensate of asthma and control subjects --- p.31 / Table 3. Levels of eotaxin and MDC in exhaled breath condensate of asthma subjects on different dose of inhaled corticosteroids --- p.33 / Figure 6. Relationship between exhaled breath condensate level of MDC and total serum IgE level --- p.35

Indiana University-Purdue University Indianapolis (IUPUI) / The patients with Cystic fibrosis (CF), an inherent genetic disorder, suffer from chronic bacterial infection in the lung. In CF, modification of epithelial cells leads to alteration of the lung environment, such as inhibition of ciliary bacterial clearance and accumulation of thickened mucus in the airways. Exploiting these conditions, opportunistic pathogens like Pseudomonas aeruginosa cause lifelong persistent infection in the CF lung by forming into antibiotic-resistant aggregated communities called biofilms. Airway infections as well as inflammation are the two major presentations of CF lung disease. P. aeruginosa strains isolated from CF lungs often contain mutations in the mucA gene, and this mutation results in higher level expression of bacterial polysaccharides and toxic lipoproteins. In a previous work, we have found a putative lipoprotein gene (PA4326) which is overexpressed in antibiotic-induced biofilm formed on cultured CF-derived airway cells. In the current work, we speculated that this particular putative lipoprotein affects cellular cytotoxicity and immune-stimulation in the epithelial cells. We found that mutation of this gene (ΔPA4326) results in reduced airway cell killing without affecting other common virulence factors.Moreover, we observed that this gene was able to stimulate secretion of the proinflammatory cytokine IL-8 from host cells. Interestingly, we also found that ΔPA4326 mutant strains produced less pyocyanin exotoxin compared to the wild type. Furthermore, our results suggest that PA4326 regulates expression of the pyocyanin biosynthesis gene phzM, leading to the reduced pyocyanin phenotype. Overall, these findings implicate PA4326 as a virulence factor in Pseudomonas aeruginosa. In the future, understating the molecular interplay between the epithelial cells and putative lipoproteins like PA4326 may lead to development of novel anti-inflammatory therapies that would lessen the suffering of CF patients.

Indiana University-Purdue University Indianapolis (IUPUI) / More than 300 million people world-wide suffer from breathlessness, wheezing, chest tightness, and coughing characteristic of chronic bronchial asthma, the global incidence of which is on the rise. Allergen-sensitization and challenge elicits pulmonary expression of chemoattractants that promote a chronic eosinophil-rich infiltrate. Eosinophils are increasingly recognized as important myeloid effectors in chronic inflammation characteristic of asthma, although few eosinophil molecular signaling pathways have successfully been targeted in asthma therapy. p21 activated kinases (PAKs), members of the Ste-20 family of serine/threonine kinases, act as molecular switches in cytoskeletal-dependent processes involved in cellular motility. We hypothesized that PAK1 modulated eosinophil infiltration in an allergic airway disease (AAD) murine model. In this model, Pak1 deficient mice developed reduced inflammatory AAD responses in vivo with notable decreases in eosinophil infiltration in the lungs and broncho-alveolar lavage fluids (BALF). To test the importance of PAK1 in hematopoietic cells in AAD we used complementary bone marrow transplant experiments that demonstrated decreased eosinophil inflammation in hosts transplanted with Pak1 deficient bone marrow. In in vitro studies, we show that eotaxin-signaling through PAK1 facilitated eotaxin-mediated eosinophil migration. Ablating PAK1 expression by genetic deletion in hematopoietic progenitors or siRNA treatment in derived human eosinophils impaired eotaxin-mediated eosinophil migration, while ectopic PAK1 expression promoted this migration. Together these data suggest a key role for PAK1 in the development of atopic eosinophil inflammation and eotaxin-mediated eosinophil migration.