Our research program can be broadly defined as developing a respiratory systems biology approach utilizing a range of ‘omics, bioinformatics, & statistical platforms to characterize molecular sub-phenotypes of chronic inflammatory lung diseases. We focus equal efforts on translational studies of the response to environmental exposures in patients with COPD and asthma, and innovation & methodology development in the fields of intact quantitative proteomics, multivariate modeling and data integration. Our translational systems medicine studies encompass profiling of mRNA, miRNA, proteomes, metabolomes and lipid mediators of from multiple lung compartments (airway epithelium, alveolar macrophages, exosomes, and bronchoalveolar exudates) using multiple omics platforms, in combination with extensive clinical phenotyping. The strength of our approaches is the ability to integrate information from multiple molecular levels, including the mRNA, miRNA, protein and metabolite levels, with rigorous clinical characterizations in order to understand disease mechanisms on a systems level.
The true power – and challenge – in these studies are the integration of the multi-molecular level screening results with in depth clinical characterizations in order to understand and categorize unknown sub-phenotypes of complex disease. Like many other complex diseases, both COPD and asthma represent umbrella diagnoses encompassing a range of underlying molecular mechanisms which all lead to a similar set of symptoms or alterations in lung function. However, the reliance on symptoms and alterations in lung function for diagnosis makes it challenging to develop diagnostic and treatment options that are efficacious across the different subgroups of patients. Molecular sub-phenotyping thus represents an essential step towards the discovery of relevant diagnostic or prognostic biomarkers and treatment options for specific patient groups, a.k.a. personalized medicine.
In the Karolinska COSMIC study, we are investigating molecular sub-phenotypes of smoking-induced COPD. A particular focus relates to recent epidemiological indications of gender differences in both incidence and severity of disease, with post-menopausal women being at greatest risk. The study encompasses profiling of mRNA, miRNA, proteomes, metabolomes and lipid mediators of from multiple lung compartments (airway epithelium, alveolar macrophages, exosomes, and bronchoalveolar exudates) using multiple omics platforms, in combination with extensive clinical phenotyping of early stage COPD patients, never-smokers, and smokers with normal lung function from both genders. The completion of the first leg of the study revealed significant differences in the macrophage proteome between COPD patients and healthy controls. These differences were entirely driven by the female population, with a subset of 19 protein biomarkers providing highly significant classification of healthy smokers from early stage COPD patients (p=10-7), with 78% predictive power (Kohler et al., JACI, 2013). These alterations in the proteome of women could be linked to specific molecular pathways related to macro-autophagy which has been associated with an airway inflammatory phenotype, thus linking our molecular results to know gender-differences in clinical phenotypes. Results from both up-stream screening of mRNA and miRNA, and down-stream screening of lipid mediator and cytokines support the existence of gender-associated molecular sub-phenotypes of COPD. By using unbiased clustering based on identified ‘omics-based COPD classifications, we can identify a sub-group of subjects among smokers with normal lung function being at elevated risk of developing COPD. This illustrates part of the beauty and vision of systems medicine; To provide prognostic molecular insight into deviations from the healthy state, rather than the traditional definitions of disease states.
In the SUBWAY study, we have investigated the molecular responses to subway air exposure in asthmatic subjects compared to healthy. Subway air contains high levels of particulate matter enriched in iron oxides, which can cause oxidative stress and subsequent release of pro-inflammatory mediators in the airway. The human subjects in this study, all naïve to previous subway exposure, were sampled through bronchoalveolar lavage (BAL) both pre- and post subway exposure to normalize for inter-individual variability. We employed a combination of miRNA profiling of exosomes (Levänen et al, JACI, 2013) and lipid mediator profiling (Lundström et al, PLoS One, 2011) from BAL fluid. The results showed that subjects with mild asthma have an impaired ability to down-regulate the initial inflammatory response towards subway air exposure, indicating a prolonged and intensified initial inflammatory reaction in asthmatics that is quickly resolved in healthy subjects. Interestingly, we also found alterations in both lipid- and miRNA profile at baseline levels in asthmatics compared to healthy, indicating a predisposition to an adverse response even in mild intermittent, stable asthma.
In the LUNAPRE study, we are using our systems medicine workflow to investigating an emerging and steadily growing subgroup of patients at elevated risk of developing early onset obstructive lung disease; survivors of bronchopulmonary dysplasia (BPD). Inflammatory conditions occurring in childhood and adolescence of very prematurely born children due to oxygen treatment and/or developmental impairments during the neonatal period often leads to obstructive disease, airway hyperreactivity, and premature decline in lung function in early adulthood. Currently this type of obstructive disease is categorized under the umbrella diagnosis COPD due to the associated symptoms and lung function impairments. However, due to the differences in etiology compared to other forms of COPD, the underlying mechanisms are likely to be distinct from e.g. smoking-induced COPD. Multi-level molecular characterization of the alterations in the lungs of BPD patients compared to relevant control groups may reveal subsets of mediators as well as molecular pathways that are critical in the pathological changes occurring in BPD- and premature birth-related obstructive lung disease.