Bulk RNA-Seq, ATAC-Seq, and scRNA-Seq of macaque alveolar macrophages with alcohol drinking

Chronic alcohol drinking is associated with increased susceptibility to viral and bacterial respiratory pathogens. Investigating the effects of alcohol on the lung is challenging in humans because of the complexity of human drinking behavior and the challenge of obtaining samples. In this study, we utilize a rhesus macaque model of voluntary ethanol self-administration to study the effects of alcohol on the lung in a physiologically and genetically relevant model. We report a heightened activation and inflammatory state in alveolar macrophages (AM) obtained from ethanol drinking animals that is accompanied by increased chromatin accessibility in intergenic regions that regulate inflammatory genes and contain binding motifs for transcription factors AP-1, IRF8, and NFKB p-65. In line with these transcriptional and epigenetic changes at basal state, AM from ethanol drinking animals generate elevated inflammatory mediator responses to LPS and respiratory syncytial virus (RSV). Alternatively, transcriptional analysis revealed an inefficient upregulation of interferon response genes with EtOH in the response to RSV. This along with baseline transcriptional downregulation and closed chromatin with EtOH mapping to tissue repair and maintenance mechanisms points to functional deficiencies in AM due to EtOH. Analysis using scRNA-Seq revealed heterogeneity in lung-resident macrophage and monocyte populations, including shifts from tissue maintenance to pathogen response clusters which could be due to altered differentiation trajectories with EtOH. Finally, increased oxidative stress induced metabolic shifts towards oxidative phosphorylation coupled with increased active mitochondria. Functionally, AM had increased cytosolic ROS and decreased ability to phagocytose bacteria. This comprehensive epigenomic, transcriptional and functional profiling of lung macrophages after ethanol drinking in macaques provides previously unidentified mechanisms of ethanol induced infection susceptibility in patients with alcohol use disorders.