In-depth Systems Biological Evaluation of Bovine Alveolar Macrophages Suggests Novel Insights into Molecular Mechanisms Underlying Infection

Objective: Bovine tuberculosis (bTB) is a chronic respiratory infectious disease of domestic livestock caused by intracellular infection, which causes ~$3 billion in annual losses to global agriculture. Providing novel tools for bTB managements requires a comprehensive understanding of the molecular regulatory mechanisms underlying the infection. Nevertheless, a combination of different bioinformatics and systems biology methods was used in this study in order to clearly understand the molecular regulatory mechanisms of bTB, especially the immunomodulatory mechanisms of infection.

Methods: RNA-seq data were retrieved and processed from 78 (39 non-infected control vs. 39 -infected samples) bovine alveolar macrophages (bAMs). Next, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules in non-infected control bAMs as reference set. The WGCNA module preservation approach was then used to identify non-preserved modules between non-infected controls and -infected samples (test set). Additionally, functional enrichment analysis was used to investigate the biological behavior of the non-preserved modules and to identify bTB-specific non-preserved modules. Co-expressed hub genes were identified based on module membership (MM) criteria of WGCNA in the non-preserved modules and then integrated with protein-protein interaction (PPI) networks to identify co-expressed hub genes/transcription factors (TFs) with the highest maximal clique centrality (MCC) score (hub-central genes).

Results: As result, WGCNA analysis led to the identification of 21 modules in the non-infected control bAMs (reference set), among which the topological properties of 14 modules were altered in the -infected bAMs (test set). Interestingly, 7 of the 14 non-preserved modules were directly related to the molecular mechanisms underlying the host immune response, immunosuppressive mechanisms of , and bTB development. Moreover, among the co-expressed hub genes and TFs of the bTB-specific non-preserved modules, 260 genes/TFs had double centrality in both co-expression and PPI networks and played a crucial role in bAMs- interactions. Some of these hub-central genes/TFs, including , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and , had potential targets for inducing immunomodulatory mechanisms by to evade the host defense response.

Conclusion: The present study provides an in-depth insight into the molecular regulatory mechanisms behind infection through biological investigation of the candidate non-preserved modules directly related to bTB development. Furthermore, several hub-central genes/TFs were identified that were significant in determining the fate of infection and could be promising targets for developing novel anti-bTB therapies and diagnosis strategies.