IDENTIFICATION OF GENE REGULATORY MODULES IN A HUMAN MODEL OF PHYSIOLOGICAL INFLAMMATION: A BIOINFORMATICS APPROACH

In healthy organisms, inflammation is the first defense mechanism and monocytes and macrophages are among the key players of this process. Since a alteration of the activity of these cell populations is at the base of several pathological conditions, elucidating the molecular mechanisms of monocyte/macrophage activation represents a major step to study inflammatory disorders and, eventually, develop new therapeutic strategies. However, these mechanisms and their interplay during monocyte/macrophage activation still remain poorly characterized. Here, we report the setup of a physiological inflammation model, based on human primary cells, and of a bioinformatics approach that allow studying the development of the inflammatory reaction during its entire course and elucidating networks of molecular interactions which are at the basis of this process. Specifically, human blood monocytes isolated from blood of normal healthy donors have been cultured and exposed to a combination of factors reproducing physiological inflammatory conditions and their gene expression profiles monitored during a time course of 48 hours. The computational process starts with the identification of those genes whose expression changes during the time course and that, through enrichment analysis, appear to be involved in inflammatory processes. These genes can be considered as controllers of the process and thus are further used as regulators to identify regulatory modules. Using these computational methods we have been able to obtain genes that characterize the various steps of the inflammatory process and to reconstruct their connection modules. Finally, to validate our results we performed a comparison between data from the physiological inflammation model and data obtained from ChIP-seq that combines chromatin immunoprecipitation with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.