The Biospecimen and Bioinformatics Core will provide a core resource for the processing, storage, and distribution of biospecimens collected from the clinical studies described in Core B and will provide integrated and advanced Bioinformatics support for "Th2-phenotyping" and additional genomic analyses proposed in the projects. The analysis of gene and protein expression in human tissues requires close attention to quality with respect to processing and storage and we have considerable experience with proven protocols for handling all of the human samples that will be collected across the projects proposed here. In addition, data analysis for mRNA and miRNA expression studies, especially those which employ high- throughput platforms such as expression microarrays or Fluidigm BioMark PCR, require specialized protocols and expertise with respect to data processing and analysis, and we have developed a formal Bioinformatics resource with optimized protocols for handling these specific data analysis challenges. Finally, the gold-standard assignment of TH2-phenotype depends on a standardized analysis of gene expression in airway epithelial brushings. Using the capabilities of this formal Biospecimen Bank and Bioinformatics resource, the core will have three specific aims: 1).To provide specialized processing, secure storage, and timely distribution of the human biospecimens collected from the clinical studies, 2) To establish the "gold- standard" assignment of Th2-phenotype to subjects enrolled in the clinical studies through analysis of airway epithelial gene expression, 3) To provide integrated and advanced bioinformatics support for additional genomic analyses proposed by each of the three projects which comprise this Program Project Grant application.

Public Health Relevance

This Core (Core C) will provide an integrated resource for the processing, storage, and distribution of biospecimens collected from the clinical studies described in Core B and will provide advanced data analysis (Bioinformatics) support for the proposed projects.

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
Research Program Projects (P01)
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Heart, Lung, and Blood Initial Review Group (HLBP)
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University of California San Francisco
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Bando, Jennifer K; Liang, Hong-Erh; Locksley, Richard M (2015) Identification and distribution of developing innate lymphoid cells in the fetal mouse intestine. Nat Immunol 16:153-60
Simpson, Laura J; Patel, Sana; Bhakta, Nirav R et al. (2014) A microRNA upregulated in asthma airway T cells promotes TH2 cytokine production. Nat Immunol 15:1162-70
Thomas, Molly F; L'Etoile, Noelle D; Ansel, K Mark (2014) Eri1: a conserved enzyme at the crossroads of multiple RNA-processing pathways. Trends Genet 30:298-307
Peters, Michael C; Mekonnen, Zesemayat K; Yuan, Shaopeng et al. (2014) Measures of gene expression in sputum cells can identify TH2-high and TH2-low subtypes of asthma. J Allergy Clin Immunol 133:388-94
Jackson, Daniel J; Hartert, Tina V; Martinez, Fernando D et al. (2014) Asthma: NHLBI Workshop on the Primary Prevention of Chronic Lung Diseases. Ann Am Thorac Soc 11 Suppl 3:S139-45
Baumjohann, Dirk; Ansel, K Mark (2014) MicroRNA regulation of the germinal center response. Curr Opin Immunol 28:6-11
von Moltke, Jakob; Locksley, Richard M (2014) I-L-C-2 it: type 2 immunity and group 2 innate lymphoid cells in homeostasis. Curr Opin Immunol 31:58-65
Locksley, Richard M; Fahy, John V (2014) Asthma and the flu: a tricky two-step. Immunol Cell Biol 92:389-91
Van Dyken, Steven J; Mohapatra, Alexander; Nussbaum, Jesse C et al. (2014) Chitin activates parallel immune modules that direct distinct inflammatory responses via innate lymphoid type 2 and ?? T cells. Immunity 40:414-24
Bronevetsky, Yelena; Ansel, K Mark (2013) Regulation of miRNA biogenesis and turnover in the immune system. Immunol Rev 253:304-16

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