Publications

BACKGROUND

Asthma is a chronic inflammatory airway disease influenced by genetic and environmental factors that affects ~300 million people worldwide, leading to ~250,000 deaths annually. Glucocorticoids (GCs) are well-known therapeutics that are used extensively to suppress airway inflammation in asthmatics. The airway epithelium plays an important role in the initiation and modulation of the inflammatory response. While the role of GCs in disease management is well understood, few studies have examined the holistic effects on the airway epithelium.

METHODS

Gene expression data were used to generate a co-transcriptional network, which was interrogated to identify modules of functionally related genes. In parallel, expression data were mapped to the human protein-protein interaction (PPI) network in order to identify modules with differentially expressed genes. A common pathways approach was applied to highlight genes and pathways functionally relevant and significantly altered following GC treatment.

RESULTS

Co-transcriptional network analysis identified pathways involved in inflammatory processes in the epithelium of asthmatics, including the Toll-like receptor (TLR) and PPAR signaling pathways. Analysis of the PPI network identified RXRA, PPARGC1A, STAT1 and IRF9, among others genes, as differentially expressed. Common pathways analysis highlighted TLR and PPAR signaling pathways, providing a link between general inflammatory processes and the actions of GCs. Promoter analysis identified genes regulated by the glucocorticoid receptor (GCR) and PPAR pathways as well as highlighted the interferon pathway as a target of GCs.

CONCLUSIONS

Network analyses identified known genes and pathways associated with inflammatory processes in the airway epithelium of asthmatics. This workflow illustrated a hypothesis generating experimental design that integrated multiple analysis methods to produce a weight-of-evidence based approach upon which future focused studies can be designed. In this case, results suggested a mechanism whereby GCs repress TLR-mediated interferon production via upregulation of the PPAR signaling pathway. These results highlight the role of interferons in asthma and their potential as targets of future therapeutic efforts.

BACKGROUND: Researchers have the potential to utilize genetic modification (GM) technologies to create a hybrid of "food" and "medicine" that may challenge traditional understandings of what is "natural". Moral and ethical concerns are likely to arise in any discussion of these therapeutic foods and will affect the integration of products into clinical care and daily life. This study examined how patients with chronic gastrointestinal (GI) diseases view probiotics as future bioengineered therapeutic foods. METHODS: A multi-site qualitative study consisting of focus groups with chronic GI diseases was conducted at Cleveland Clinic, Mayo Clinic, and Johns Hopkins University RESULTS: We conducted twenty-two focus groups with 136 patients with major GI diseases between March and August 2009. GI patients associated the term "natural" with concepts of diminished risk and morally "good"; conversely, patients associated the term "unnatural" with things that are "risky," "foreign", and morally "bad". Readily available unmodified probiotics were more commonly described as "natural" while genetically modified probiotics were more commonly labeled as "unnatural" and "risky". However, patients acknowledged that not all natural products are safe, nor are unnatural products always harmful. CONCLUSIONS: If GI patient perspectives are indicative of public perceptions of therapeutic foods, our findings suggest that the potential benefits and risks of clinical and public health initiatives employing therapeutic foods will be understood in moralistic terms. Bioethicists and others should be sensitive to the implicit normative appeals that are often embedded in the language of what is "natural" and "unnatural".