Diesel exhaust particles dysregulate multiple immunological pathways in murine macrophages: Lessons from microarray and scRNA-seq technologies

Authors: BHETRARATANA, MAY - University Of California (UCLA); OROZCO, LUZ - University Of California (UCLA); HONG, JASON - University Of California (UCLA); DIAMANTE, GRACIAL - University Of California (UCLA); MAJID, SANA - University Of California (UCLA); Bennett, Brian; AHN, IN SOOK - University Of California (UCLA); YANG, XIA - University Of California (UCLA); LUSIS, ALDONS - University Of California (UCLA); ARAUJO, JESUS - University Of California (UCLA)

Submitted to: Archives of Biochemistry and Biophysics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/24/2019
Publication Date: 9/27/2019
Citation: Bhetraratana, M., Orozco, L.D., Hong, J., Diamante, G., Majid, S., Bennett, B.J., Ahn, I., Yang, X., Lusis, A.J., Araujo, J.A. 2019. Diesel exhaust particles dysregulate multiple immunological pathways in murine macrophages: Lessons from microarray and scRNA-seq technologies . Archives of Biochemistry and Biophysics. https://doi.org/10.1016/j.abb.2019.108116.
DOI: https://doi.org/10.1016/j.abb.2019.108116

Interpretive Summary: Macrophages are immune cells that respond to environmental stimuli and often initiate inflammation. Macrophage response is critical in the development of inflammatory processes in the lungs and in the cardiovascular system leading to atherosclerosis. Diet and pollutants are environmental stimuli that induce macrophage inflammation and have been implicated in obesity and cardiovascular disease. In the current study, we aimed to characterize macrophage responses induced by diesel exhaust particles in vitro and in vivo. Our studies focus on the identification of genes and pathways altered in response to stimuli. To do this we utilize transcriptomic approaches, single-cell RNA sequencing and RmRNA microarrays, to elucidate genome-wide changes following treatment of peritoneal macrophages in culture. Both approaches allowed us to identify robust effects on macrophage activation and inflammation.

Technical Abstract: Exposure to ambient particulate matter has been shown to promote cardiovascular diseases, predominantly of ischemic character. However, the mechanisms linking inhaled particulates with systemic vascular effects resulting in worsened atherosclerosis are not well defined. We assessed the potential role of macrophages in translating these effects by analyzing gene expression patterns in response to diesel exhaust particles (DEP) at the average cell level using Affymetrix microarrays and at the individual cell level using single-cell RNA sequencing (scRNA-seq). Peritoneal macrophages, harvested from C57BL/6J mice and treated with 25 µg/mL of a DEP methanol extract (DEPe) exhibited significant differential expression of a large number of genes, particularly enriched in antioxidant and immune pathways as judged by Affymetrix microarray analysis. This in vitro work allowed us to predict in vivo responses displayed by C57BL/6J mice subjected to oropharyngeal instillation of 200 µg of whole DEP. The gene expression profile of their alveolar macrophages was analyzed at the single-cell level using scRNA-seq, which showed significant dysregulation of a broad number of genes enriched in immune system pathways as well. The scRNA-seq data also demonstrated large heterogeneity in how individual alveolar macrophages respond to DEP exposures.