In the prior funding period, the Biospecimen and Bioinformatics Core (Core C) was extremely productive in its development of new methods and provision of an essential core resource for the processing, storage, and distribution of biospecimens collected from the clinical studies and advanced Bioinformatics support for ?Type 2 inflammatory phenotyping? and genomic analyses. In this funding period, the Biospecimen and Bioinformatics Core will continue to provide essential processing, storage, and distribution of biospecimens collected from the clinical studies funded by this grant and will refine mass cytometry (CyTOF protocols) and perform new services related to mass cytometry (CyTOF). These CyTOF services include development and validation of CyTOF panels and CyTOF staining of the experimental samples. The Core?s Bioinformatics resource also has optimized pipelines for handling the new data analysis challenges related to CyTOF and will provide specialized cross- investigator integrated analyses of bulk RNA-seq, single cell sequencing, ATAC-seq and DNA methylation studies proposed in the projects. Core C will integrate these analyses using scientific input from all 3 projects and perform iterative analyses across experiments and experimental groups. Finally, this core will share banked samples from the IRB-approved existing UCSF Airway Tissue Bank to the Projects of this P01. The Bioinformatics Core will have an extension at National Jewish Health led by Max A. Seibold, who is also a Co-I for Project 3. It will also have expert input on CyTOF from Dr. Matthew Spitzer (a Co-I on the Core) and expert input on single cell RNA-seq analyses from Dr. David Erle (a consultant/collaborator).
The proposed research is relevant to public health because asthma is a common medical condition, severe asthma accounts for great public health burden and cost, and further advancing effective treatment of severe asthma will depend on identifying the biological mechanisms underlying the persistence of type 2 inflammation in the airway. Successful completion of the work proposed in this Core will provide each of the associated projects with the clinical samples, perform advanced cell staining protocols (CyTOF) and provide advanced biostatistical support for genomics analyses.
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| Pavord, Ian D; Beasley, Richard; Agusti, Alvar et al. (2018) After asthma: redefining airways diseases. Lancet 391:350-400 |
| Lachowicz-Scroggins, Marrah E; Gordon, Erin D; Wesolowska-Andersen, Agata et al. (2018) Cadherin-26 (CDH26) regulates airway epithelial cell cytoskeletal structure and polarity. Cell Discov 4:7 |
| Bhakta, Nirav R; Christenson, Stephanie A; Nerella, Srilaxmi et al. (2018) IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma. Am J Respir Crit Care Med 197:313-324 |
| Peters, Michael C; Ringel, Lando; Dyjack, Nathan et al. (2018) A Transcriptomic Method to Determine Airway Immune Dysfunction in T2-High and T2-Low Asthma. Am J Respir Crit Care Med : |
| Wong-McGrath, Kelly; Denlinger, Loren C; Bleecker, Eugene R et al. (2018) Internet-Based Monitoring in the Severe Asthma Research Program Identifies a Subgroup of Patients With Labile Asthma Control. Chest 153:378-386 |
| Van Dyken, Steven J; Locksley, Richard M (2018) Chitins and chitinase activity in airway diseases. J Allergy Clin Immunol 142:364-369 |
| Dunican, Eleanor M; Elicker, Brett M; Gierada, David S et al. (2018) Mucus plugs in patients with asthma linked to eosinophilia and airflow obstruction. J Clin Invest 128:997-1009 |
| Fassett, Marlys S; Pua, Heather H; Simpson, Laura J et al. (2018) Identification of Functionally Relevant microRNAs in the Regulation of Allergic Inflammation. Methods Mol Biol 1799:341-351 |
| Schneider, Christoph; O'Leary, Claire E; von Moltke, Jakob et al. (2018) A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling. Cell 174:271-284.e14 |
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