Proteomics of lung cell biology and pulmonary disease

Proteomics has the goal of defining the complete protein complement of biological systems, which can then be analyzed in a comparative fashion to generate informative data regarding protein expression and function. Proteomic analyses can also facilitate the discovery of biomarkers that can be used to diagnose and monitor disease severity, activity and therapeutic response, as well as to identify new targets for drug development. A major challenge for proteomics, however, has been detecting low-abundance proteins in complex biological fluids. This review summarizes how proteomic analyses have advanced lung cell biology and facilitated the identification of new mechanisms of disease pathogenesis in respiratory disorders, such as asthma, cystic fibrosis, lung cancer, acute lung injury and sarcoidosis. The impact of nanotechnology and microfluidics, as well as studies of post-translational modifications and protein-protein interactions (the interactome), are considered. Furthermore, the application of systems-biology approaches to organize and analyze data regarding the lung proteome, interactome, genome, transcriptome, metabolome, glycome and small RNAome (regulatory RNAs), should facilitate future conceptual advances regarding lung cell biology, disease pathogenesis, biomarker discovery and drug development.