Work package 10
Mechanistic studies into repair defects in chronic lung disease using advanced models and analyzing biomarkers identified in the PRIL cohort
Once the advanced models for lung repair have been developed in WP3, and after obtaining possible biomarkers for early lung damage from WP1/5/6/7, we aim to gain more insight in abnormal damage and repair responses to environmental exposures in lung disease.
The first aim of this work package is to provide novel insight in abnormal repair responses in lung disease upon environmental exposures using advanced models. The second aim is identification of extra-pulmonary tissue derived protective and damaging features of the metabolic milieu in these models.
By comparison of repair responses between cultures from well-characterized COPD patients (at high risk) and those from controls, we aim to provide novel insight in abnormal repair responses in lung disease upon environmental exposures. We will monitor real-time secretion profiles of cytokines/danger signals, growth factors and other markers for damage/repair. Specifically, we will also monitor the gene expression and/or real-time secretion profiles of the biomarkers identified in the PRIL cohort using 3D models and/or organ-on-a-chip approaches.
Additionally, at specific time points, we will collect RNA from our co-culture models and lung slices to study for next generation RNA sequencing (RNASeq), a highly sensitive high-throughput approach in order to investigate the mechanisms that underlie aberrant repair responses by assessing differences in gene expression profiles between control tissue and that of patients.
In the second aim of this work package, the metabolic interaction between extra-pulmonary tissue (including skeletal muscle) and lung cells will be investigated using novel cell culture models based on lab-on-chip approaches developed in WP3. The muscle secretome will be altered by physiological relevant stimuli, and protective or sensitizing effects on damage or repair responses (as defined in WP 2 and WP3) of co-cultured alveolar progenitors exposed to noxious compounds will be assessed.
In addition, 3D cultured human skeletal muscle (hSM) cell lines will be maintained in homeostasis, or stressed by established inducers of muscle dysfunction (stimulating loss of mass and oxidative capacity). Integrative -omics analyses of the hSM secretome will be deployed for identification of differentially secreted metabolites and myokines that may represent a potential protective or unfavorable metabolic milieu for lung responses to the exposome. The presence of these systemically released factors will be assessed in serum of the PRIL cohort, and correlated to the development of disease.
The deliverable of this work package is insight into defective repair mechanisms in chronic lung disease and novel therapeutic targets to improve lung repair. These data will be integrated with the outcomes of WP2, 3 and WP8. This will provide further insight in the genes and pathways involved in abnormal repair responses in chronic lung disease. Factors that will be identified in this work package will also be assessed in the PRIL cohort (WP6) and will be tested in intervention studies (WP11).