Genomes and Genes
David J Erle
Affiliation: University of California
- Use of spotted oligonucleotide arrays for large-scale analysis of mammalian gene expressionDavid J Erle
Functional Genomics Core Facility, UCSF Sandler Center for Basic Research in Asthma, University of California, San Francisco, San Francisco, CA, USA
Chest 121:80S. 2002
- Asthma investigators begin to reap the fruits of genomicsDavid J Erle
Lung Biology Center, Department of Medicine, University of California, San Francisco, CA 94143, USA
Genome Biol 4:232. 2003..Microarray experiments have identified novel candidate genes in animal models of asthma. In the near future, genomics may have a profound impact on the way we think about this common and complex disease...
- The epithelial anion transporter pendrin is induced by allergy and rhinovirus infection, regulates airway surface liquid, and increases airway reactivity and inflammation in an asthma modelYasuhiro Nakagami
Lung Biology Center, Department of Medicine, University of California, San Francisco, CA 94158, USA
J Immunol 181:2203-10. 2008..We conclude that pendrin regulates ASL thickness and may be an important contributor to asthma exacerbations induced by viral infections or allergens...
- AGR2 is induced in asthma and promotes allergen-induced mucin overproductionBradley W Schroeder
Lung Biology Center, Department of Medicine, University of California San Francisco, USA
Am J Respir Cell Mol Biol 47:178-85. 2012..AGR2 interacts with immature mucin in the ER and loss of AGR2 impairs allergen-induced MUC5AC and MUC5B overproduction...
- Distinct roles of FOXA2 and FOXA3 in allergic airway disease and asthmaSung Woo Park
Lung Biology Center, University of California San Francisco, San Francisco, California 94143, USA
Am J Respir Crit Care Med 180:603-10. 2009..IL-13-driven mucous cell metaplasia is associated with decreased expression of the transcription factor FOXA2 and increased expression of the related transcription factor FOXA3 in animal and cell culture models...
- A distinctive alveolar macrophage activation state induced by cigarette smokingPrescott G Woodruff
UCSF Mission Bay Rock Hall, Room 545, 1550 4th Street, San Francisco, CA 94158, USA
Am J Respir Crit Care Med 172:1383-92. 2005..Macrophages are believed to play a central role in emphysema based largely on data from mouse models. However, the relevance of these models to smoking-related lung disease in humans is uncertain...
- The cell biology of asthmaDavid J Erle
Lung Biology Center and Department of Medicine, University of California, San Francisco, San Francisco, CA 94143
J Cell Biol 205:621-31. 2014....
- The protein disulfide isomerase AGR2 is essential for production of intestinal mucusSung Woo Park
Lung Biology Center and Program in Immunology, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 106:6950-5. 2009..We conclude that AGR2 is a unique member of the PDI family, with a specialized and nonredundant role in intestinal mucus production...
- Dissecting asthma using focused transgenic modeling and functional genomicsDouglas A Kuperman
Department of Medicine, Allergy Immunology Division, Northwestern University Feinberg School of Medicine, Chicago, USA
J Allergy Clin Immunol 116:305-11. 2005..These mice develop airway hyperreactivity and mucus overproduction but not airway inflammation...
- Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroidsPrescott G Woodruff
Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 104:15858-63. 2007....
- IL-13 and epidermal growth factor receptor have critical but distinct roles in epithelial cell mucin productionGuohua Zhen
Department of Medicine, University of California, San Francisco, CA 94143 2922, USA
Am J Respir Cell Mol Biol 36:244-53. 2007....
- The αvβ6 integrin modulates airway hyperresponsiveness in mice by regulating intraepithelial mast cellsKotaro Sugimoto
Lung Biology Center, Department of Medicine, UCSF, San Francisco, California, USA
J Clin Invest 122:748-58. 2012....
- Systemically dispersed innate IL-13-expressing cells in type 2 immunityApril E Price
Howard Hughes Medical Institute, Department of Medicine, University of California, San Francisco, CA 94143 0795, USA
Proc Natl Acad Sci U S A 107:11489-94. 2010..Widely dispersed innate type 2 helper cells, which we designate Ih2 cells, play an integral role in type 2 immune responses...
- Molecular basis of selective atrial fibrosis due to overexpression of transforming growth factor-β1Dolkun Rahmutula
Division of Cardiology, University of California, San Francisco, CA 94143, USA
Cardiovasc Res 99:769-79. 2013..This study investigated the role of TGF-β1 in human AF and the mechanism of atrial-selective fibrosis...
- Airway epithelial miRNA expression is altered in asthmaOwen D Solberg
Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
Am J Respir Crit Care Med 186:965-74. 2012..Changes in airway epithelial cell differentiation, driven in part by IL-13, are important in asthma. Micro-RNAs (miRNAs) regulate cell differentiation in many systems and could contribute to epithelial abnormalities in asthma...
- T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the microRNA repertoireYelena Bronevetsky
Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
J Exp Med 210:417-32. 2013....
- Integrin beta6 mediates phospholipid and collectin homeostasis by activation of latent TGF-beta1Laura L Koth
Lung Biology Center, Department of Medicine, San Francisco General Hospital, California, USA
Am J Respir Cell Mol Biol 37:651-9. 2007..These findings show that alphavbeta6 and TGF-beta1 regulate homeostasis of phospholipids and collectins in adult mouse lungs and may have implications for anti-fibrotic therapeutics that inhibit active TGF-beta in the lung...
- The transcriptional regulator Aire coopts the repressive ATF7ip-MBD1 complex for the induction of immunotoleranceMichael Waterfield
1 Diabetes Center, University of California San Francisco, San Francisco, California, USA 2 Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
Nat Immunol 15:258-65. 2014....
- IL-4 receptor signaling in Clara cells is required for allergen-induced mucus productionDouglas A Kuperman
Lung Biology Center, Department of Medicine, University of California, San Francisco, CA 94143, USA
J Immunol 175:3746-52. 2005..Because only IL-13 and IL-4 are thought to signal via IL-4Ralpha, we conclude that direct effects of IL-4 and/or IL-13 on Clara cells are required for allergen-induced mucus production in the airway epithelium...
- Direct effects of interleukin-13 on epithelial cells cause airway hyperreactivity and mucus overproduction in asthmaDouglas A Kuperman
Lung Biology Center, Department of Medicine and Cardiovascular Research Institute, University of California San Francisco School of Medicine, San Francisco, California, USA
Nat Med 8:885-9. 2002..These results demonstrate the importance of direct effects of IL-13 on epithelial cells in causing two central features of asthma...
- Differential gene expression by integrin beta 7+ and beta 7- memory T helper cellsMadeleine W Rodriguez
Department of Medicine, University of California, San Francisco, CA 94143 0854, USA
BMC Immunol 5:13. 2004..We hypothesized that beta 7+ and beta 7- blood memory T helper cells differ in their expression of genes that play a role in the adhesion or migration of T cells...
- Squamous metaplasia amplifies pathologic epithelial-mesenchymal interactions in COPD patientsJun Araya
Department of Pathology, Lung Biology Center, UCSF, San Francisco, California 94110, USA
J Clin Invest 117:3551-62. 2007..Our findings have identified TGF-beta as a potential therapeutic target for COPD...
- Increased DNA microarray hybridization specificity using sscDNA targetsChristopher S Barker
Gladstone Institute of Cardiovascular Disease, The J David Gladstone Institutes, San Francisco, California 94158, USA
BMC Genomics 6:57. 2005....
- The Th2 lymphocyte products IL-4 and IL-13 rapidly induce airway hyperresponsiveness through direct effects on resident airway cellsRajeev Venkayya
Lung Biology Center, Program in Immunology, University of California San Francisco, Box 0854, San Francisco, CA 94143 0854, USA
Am J Respir Cell Mol Biol 26:202-8. 2002..These results strongly suggest that products of activated Th2 lymphocytes can rapidly perturb airway function through direct effects on resident airway cells...
- Massively parallel functional annotation of 3' untranslated regionsWenxue Zhao
Lung Biology Center, University of California San Francisco, San Francisco, California, USA
Nat Biotechnol 32:387-91. 2014..This work shows how massively parallel approaches can improve the functional annotation of noncoding sequences, advance our understanding of cis-regulatory mechanisms and quantify the effects of human genetic variation. ..
- Age-dependent hepatic lymphoid organization directs successful immunity to hepatitis BJean Publicover
Department of Medicine, UCSF, San Francisco, California, USA
J Clin Invest 123:3728-39. 2013..Taken together, these results identify some of the immunological mechanisms necessary for effective control of HBV. ..
- Aspergillus antigen induces robust Th2 cytokine production, inflammation, airway hyperreactivity and fibrosis in the absence of MCP-1 or CCR2Laura L Koth
Lung Biology Center, Department of Medicine, University of California, San Francisco, California, USA
Respir Res 5:12. 2004..Furthermore, MCP-1-deficient mice have not previously been studied in models of experimental allergic asthma...
- The mammalian target of rapamycin regulates cholesterol biosynthetic gene expression and exhibits a rapamycin-resistant transcriptional profileBeatrice T Wang
Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 108:15201-6. 2011..PP242 caused 1,666 genes to be differentially expressed whereas rapamycin affected only 88 genes. Our analysis provides a genomewide view of the transcriptional outputs of mTOR signaling that are insensitive to rapamycin...
- Impact of the TCR signal on regulatory T cell homeostasis, function, and traffickingJoong Kyu Kim
Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
PLoS ONE 4:e6580. 2009..The results make clear multiple aspects of Treg cell homeostasis and phenotype that are dependent on a sustained capacity to signal through the TCR...
- Dissecting the tumor myeloid compartment reveals rare activating antigen-presenting cells critical for T cell immunityMiranda L Broz
Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
Cancer Cell 26:638-52. 2014..This cell type presents opportunities for prognostic and therapeutic approaches across multiple cancer types. ..
- Spotted long oligonucleotide arrays for human gene expression analysisAndrea Barczak
Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
Genome Res 13:1775-85. 2003..The approach described here involves far more gene expression measurements and provides a useful method for comparing existing and emerging techniques for genome-scale expression analysis...
- A tissue checkpoint regulates type 2 immunitySteven J Van Dyken
Department of Medicine, University of California, San Francisco, San Francisco, California, USA
Nat Immunol 17:1381-1387. 2016..Our findings suggest a mechanism by which diverse perturbations can activate type 2 immunity and reveal a shared local-tissue-elicited checkpoint that can be exploited to control both innate and adaptive allergic inflammation...
- Increased expression of neutrophil-related genes in patients with early sepsis-induced ARDSKirsten Neudoerffer Kangelaris
Department of Medicine, Division of Hospital Medicine, University of California San Francisco, San Francisco, California
Am J Physiol Lung Cell Mol Physiol 308:L1102-13. 2015..In addition, identifiable gene expression differences occurring early in the course of sepsis-related ARDS may further elucidate understanding of the neutrophil-related mechanisms in progression to ARDS...
- Toward a systematic understanding of mRNA 3' untranslated regionsWenxue Zhao
Department of Medicine, University of California, San Francisco, CA, USA
Proc Am Thorac Soc 8:163-6. 2011..Application of new data sets and experimental approaches should provide powerful insights into how 3' UTR-mediated regulatory events contribute to disease and may inspire novel therapeutic approaches...
- The asthma channel? Stay tuned . . David J Erle
Am J Respir Crit Care Med 173:1181-2. 2006
- Abnormal alveolar development associated with elevated adenine nucleosidesSuman K Banerjee
Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, 6431 Fannin, Houston, TX 77030, USA
Am J Respir Cell Mol Biol 30:38-50. 2004..These studies provide evidence that elevated lung adenosine can lead to abnormal alveogenesis by disrupting patterns of cell proliferation and apoptosis...
- Disease-specific gene expression profiling in multiple models of lung diseaseChristina C Lewis
Cincinnati Children s Hospital Medical Center Division of Immunobiology, 3333 Burnet Avenue, MLC 7038, Cincinnati, OH 45229, USA
Am J Respir Crit Care Med 177:376-87. 2008..However, analyses of individual diseases or models of diseases frequently yield extensive lists of differentially expressed genes with uncertain relationships to disease pathogenesis...
- Progress toward a systems biology approach to acute lung injuryJames A Frank
Am J Physiol Lung Cell Mol Physiol 293:L290-1. 2007
- Genomics and proteomics of lung disease: conference summaryJ Usha Raj
Division of Neonatology, Harbor UCLA Medical Center, Geffen School of Medicine at University of California, and Los Angeles Biomedical Research Institute, Los Angeles, California, USA
Am J Physiol Lung Cell Mol Physiol 293:L45-51. 2007
- Influenza virus infection causes global respiratory tract B cell response modulation via innate immune signalsW L William Chang
Center for Comparative Medicine and
J Immunol 178:1457-67. 2007....