Identification of gene expression signatures and cellular signalling pathways differentiating human monocyte subsets in community-acquired pneumonia

Abstract

Pneumonia continues to be a major global contributor to morbidity and mortality. Although antimicrobial therapy saves lives, patients frequently face complications such as sepsis and unfavourable prognoses. Increasing evidence supports the development of cell-type-specific adjuvants to enhance outcomes for pneumonia patients. Monocytes, pivotal in orchestrating the immune response during pneumonia, can adopt diverse functional states that either amplify inflammation or promote its resolution. Elucidating the mechanisms governing monocyte plasticity in vivo is essential for designing potential monocyte-targeted adjuvants. The hypothesis of the study is that a gene co-expression network model can assist in identifying cellular pathways that regulate the development of diverse monocyte functional states. The main objective of this study was to analyse bulk RNA-sequencing and flow cytometry data of blood monocytes purified from pneumonia patients on hospitalisation (acute stage) and after a 1-month follow-up (recovery), as well as from age and sex-matched control participants obtained from the public domain. Data was analysed by means of an integrative bioinformatics approach, to identify genes associated with classical, intermediate, and non-classical monocyte subsets and to define cellular biological pathways differentiating monocyte subsets. Using weighted gene co-expression network analysis, over 7000 genes were clustered into 13 co-expression modules, 7 of which were significantly correlated to one or more monocyte subsets. One module (purple) was significantly correlated to all three monocyte subsets and was enriched for the “IL-6 JAK STAT3 Signalling” and “Complement” Hallmarks gene sets as well as 6 other Immunologic Signature gene sets in GSEA. Moreover, 7 gene co-expression modules were associated with co-morbidities, including COPD and type II diabetes, as well as sepsis, a severe complication of infection. This study’s exploration of classical, intermediate and non-classical monocyte subsets in the context of pneumonia provides a more profound understanding of potentially key drivers of monocyte function, which may aid in the search for possible biomarkers as well as the development of new therapies for pneumonia.