Searching for Protein Biomarkers of Disease in Bronchoalveolar Lavage Fluid

Abstract

Thesis (Ph.D.)--University of Washington, 2012Respiratory diseases minimize gas exchange at the alveoli and complicate the mechanics of breathing. Bronchoalveolar lavage fluid (BALF) is capable of sampling the components of the alveolar epithelial lining fluid (ELF) and determining the composition of the pulmonary airways. Comprehensively profiling the proteomic landscape of BALF provides a means to understanding basic pathogenic mechanisms with the potential to develop techniques for early diagnosis in diseases concerned with lung function. Combining shotgun proteomic analysis with computational methods is a powerful approach to generate large and integrated sets of data independent of investigator's biases. This integrative methodology identifies distinct protein signatures that could be utilized as diagnostic classifiers, provide insights into the pathogenesis of lung disorder, and elucidate unsuspected mediators or pathways indicative of lung diseases. Ventilator-associated pneumonia (VAP) is defined as pneumonia occurring after 48 hours of mechanical ventilation. It is a major cause of morbidity and mortality in critically ill patients. VAP affects 8-28% of patients receiving mechanical ventilation and has a mortality rate ranging from 24% to as high as 76% in certain settings. Clinical diagnosis of VAP is challenging since the classic symptoms of pneumonia, i.e., fever, abnormal radiographs, and elevated blood cell counts are not specific for VAP among ventilated patients. Inaccurate diagnosis of VAP leads to incorrect treatment and subsequent complications related to therapy. Additionally, the lung is an important reservoir of human immunodeficiency virus (HIV) and site of HIV replication. HIV is uniformly detected in alveolar macrophages of pediatric patients and in the majority of adult patients. In addition to the numerous opportunistic infections that affect the lung, HIV directly causes significant pulmonary pathology, including lymphoid interstitial pneumonitis (LIP), nonspecific pneumonitis (NSIP), or lymphocytic alveolitis. LIP occurs in up to 75% of the pediatric population. Most HIV-infected adults develop an asymptomatic lymphocytic alveolitis, which can progress to NSIP or LIP. There is strong evidence that HIV itself evokes a local immune response that facilitates lymphocytic migration and infiltration in the lung. The pathogenesis of non-infectious pulmonary complications, following HIV infection is not fully understood. Protein profiles of BALF were determined in populations of normal, HIV and ALI (VAP+/-) volunteers. Comparative analysis identified a set of protein signatures specific to disease states. A limited protein classifier was identified and validated in the VAP study which may aid in future diagnostic endeavors. In addition, the protein profiles distinctive to HIV suggest a role that HIV-induced immunosuppression plays in the development of lung complications