Allan R Brasier, MD

4246 Health Sciences Learning Center
750 Highland Ave
Madison, WI 53705
Focus Groups: 
Signal Transduction
University of California, San Francisco
Research Summary: 
The primary focus of the work in my lab centers on mucosal diseases in the airways. Mucosal surfaces, such as the airways, are under constant attack by bacterial and viral pathogens. The first line of protection against these pathogens is mediated by a “nonspecific” immune response, termed innate immunity. Innate immunity response is an inflammatory response by the recognition of molecular patterns indicating the presence of replicating organisms. These molecular patterns are recognized by pattern recognition receptors on the surface of epithelial cells and others. Once triggered, pattern recognition receptors produce the expression of inflammatory and anti-viral genes by the epithelium. These proteins result in shaping the adaptive immune response important in specific immunity. Our studies have demonstrated the central role of a transcription factor, termed NFB, and the mechanism how it activates inflammatory gene expression. Our work shows that NFB activates a rapid, regulated gene expression mechanism termed “transcriptional elongation” to mediate innate response. Not only does this pathway provide acute response to new viral infections, our studies have shown that the NFB pathway controls cellular reprogramming, cell-state transition and remodeling/fibrosis. Major themes of my research include: 1. Innate signaling in viral induced airway disease. 2. Systems level studies of the NFB-BRD4 pathway. 3. Role of NFB-BRD4 in mesenchymal cell-state transition.
Research Detail: 

1. Innate signaling in viral induced airway disease.  A majority of my effort has focused on elucidating intracellular signal transduction pathways mediating cellular response to stress.  In a series of collaborative experiments, we were the first to demonstrate the effect of RSV replication on NFkB translocation in infected epithelial cells.  Our group has contributed to this exploding field through studying mechanisms controlling trans-activation of the NFkB transcription factor by identification of a family of inducible ribosomal S6 kinases (RS6Ks) that phosphorylate NFkB subunit RelA on a specific serine residue.  We were the first to demonstrate that the ROS signaling pathway is mediated by DNA damage response, via the ataxia telangiectasia kinase (ATM) and oxoguanine DNA glycosylase, OGG1.  Our interest in RelA Ser 276 phosphorylation is based on the finding that this post-translational modification modifies NFkB’s association with the positive transcriptional elongation complex, a complex including the epigenetic reader (and histone acetyltransferase) bromodomain 4 (BRD4) . Our more recent work has demonstrated that the BRD4 coactivator plays a major role in global activation of NFkB dependent genes, the IRF-RIG-I cross-talk pathway and interferon response genes.  Current questions being examined include the role of the epithelium in controlling the innate inflammatory response using tissue specific inducible Cre-Lox systems.​

2. Systems level studies of the NFkB-BRD4 pathway. Through NHLBI- and NIAID-funded proteomics centers, my center developed an integrated systems-level approach focusing on the NFkB network in airway epithelial cells using RNA-Seq, chromatin immunoprecipitation (ChIP)- Seq, and protein interaction studies.  In these studies, we have developed new statistical and informatics tools to interpret and understand the high throughput data.  These methods include improvements in inferring gene regulatory networks from ChIP-seq studies, based on signatures of active promoters from ENCODE data bases. We developed methods for statistical inference of error using mixed effects modeling.  More recently, we used unbiased proteomic studies of NFkB, CDK9 and BRD4 interactomes.  This latter work informed our understanding that groups of modulators are coupled to different gene expression modes that control distinct biological pathways. Current questions being examined include the BRD4 interactome and how it is activated by innate signaling.

3. Role of NFkB-BRD4 in airway remodeling. It has been observed clinically that repetitive allergen and viral exposures produce structural (fibrotic) changes in airway cells, a process referred to as airway remodeling, associated with decreased lung function.  Remodeling involves structural changes of the airway including mesenchymal transition, expansion of the myofibroblast population, and enhanced extracellular matrix production.

To understand this process mechanistically, we have observed that type II EMT, mesenchymal transition of primary cells, is mechanistically distinct from the better-studied type III EMT, mesenchymal transition of transformed cells, because distinct gene regulatory networks are activated.  In this model, we have implicated the NFkB-BRD4 pathway as a major pathway controlling the core mesenchymal gene expression system.  We have demonstrated in vivo that that persistent activation of the innate pathway by viral or allergens induces mesenchymal transition, myofibroblast expansion and fibrosis in an animal model.  This observation provides a mechanistic link for how frequent viral induced airway exacerbations are linked to airway remodeling and disease progression.  We have established an active collaboration with medicinal chemists to identify novel small molecule inhibitors of BRD4.

Selected Publications: 
B. Tian, K. Hosoki, Z. Liu, J. Yang, Y. Zhao, H. Sun, J. Zhou, E. Rytting, L. Kaphalia, W. J. Calhoun, S. Sur and AR Brasier. Mucosal bromodomain-containing protein 4 mediates aeroallergen-induced inflammation and remodeling. The Journal of allergy and clinical immunology, 6749(18)31438-6. (2019).
B. Tian, Z. Liu, J. Litvinov, R. Maroto, M. Jamaluddin, E. Rytting, I. Patrikeev, L. Ochoa, G. Vargas, M. Motamedi, BT Ameredes, J. Zhou and AR Brasier. Efficacy of Novel Highly Specific Bromodomain-Containing Protein 4 Inhibitors in Innate Inflammation-Driven Airway Remodeling. Am J Respir Cell Mol Biol. 2019 60(1):68-83.
B. Tian, Z. Liu, J. Yang, H. Sun, Y. Zhao, M. Wakamiya, H. Chen, E. Rytting, J. Zhou and AR Brasier. Selective Antagonists of the Bronchiolar Epithelial NF-kappaB-Bromodomain-Containing Protein 4 Pathway in Viral-Induced Airway Inflammation. Cell Rep 23, 1138-1151 (2018).
B. Tian, S. G. Widen, J. Yang, T. G. Wood, A. Kudlicki, Y. Zhao and AR Brasier. The NFkappaB subunit RELA is a master transcriptional regulator of the committed epithelial-mesenchymal transition in airway epithelial cells. J Biol Chem 293, 16528-16545 (2018).
B. Tian, I. Patrikeev, L. Ochoa, G. Vargas, K. K. Belanger, J. Litvinov, I. Boldogh, B. T. Ameredes, M. Motamedi and AR Brasier. NF-kappaB Mediates Mesenchymal Transition, Remodeling, and Pulmonary Fibrosis in Response to Chronic Inflammation by Viral RNA Patterns. Am J Respir Cell Mol Biol 56, 506-520 (2017).
Yang J, Tian B, Sun H, Garofalo R, Brasier AR. ZEB1 mediated epigenetic silencing of IRF1 dysregulates type III interferon responses to respiratory virus infection in epithelial to mesenchymal transition. Nature Microbiology. 2017; 2:17086.
Tian B, Yang J, Zhao Y, Ivanciuc T, Sun H, Garofalo RP, Brasier AR. Bromodomain Containing 4 (BRD4) Couples NFκB/RelA With Airway Inflammation And The IRF-RIG-I Amplification Loop In Respiratory Syncytial Virus Infection. J Virol. 2017; 91:e00007-17. PMID: 28077651.
B. Tian, I. Patrikeev, L. Ochoa, G. Vargas, K. K. Belanger, J. Litvinov, I. Boldogh, B. T. Ameredes, M. Motamedi and AR Brasier. NF-kappaB Mediates Mesenchymal Transition, Remodeling, and Pulmonary Fibrosis in Response to Chronic Inflammation by Viral RNA Patterns. Am J Respir Cell Mol Biol 56, 506-520 (2017).
Tian B, Zhao Y, Sun H, Zhang Y, Yang J, Brasier AR. BRD4 Mediates NFB-dependent Epithelial-Mesenchymal Transition and Pulmonary Fibrosis via Transcriptional Elongation. Am J Physiol Lung Cell Mol Physiol. 2016; 311(6):L1183-L1201.
Yang J, Zhao Y, Kalita M, et al. Systematic Determination of Human Cyclin Dependent Kinase (CDK)-9 Interactome Identifies Novel Functions in RNA Splicing Mediated by the DDX5/17 RNA Helicases. Molecular & cellular proteomics : Mol Cell Proteomics, 14:2701-212015. 2015.