Yan Xu, PhD
Title
Associate Professor
Director of Bioinformatics - Microarray Core
Appointment
Associate Professor of Pediatrics, University of Cincinnati College of Medicine
Email
yan.xu@cchmc.org
Phone
513-636-8921
Fax
513-636-7868
Bio
Dr. Xu is an associate professor in the Department of Pediatrics, Divisions of Pulmonary Biology and Biomedical Informatics. Her main research interests are bioinformatics applications and systems biology. She is currently focusing on the identification of gene signatures, regulatory networks and biological pathways controlling 1) surfactant homeostasis, 2) lung maturation and 3) lung cell type specific signaling. Her research goal is to integrate the data and information from new computational methods and experimental approaches in a synergistic way to gain better understanding of molecular mechanisms underlying lung development and pathogenesis.
Credentials
BS: Pharmacology, Shanghai Medical University, China, 1986.
MS: Pathology, Shanghai Medical University, China, 1989.
PhD: Molecular and Cellular Pharmacology, University of South Alabama, Mobile, Alabama, 1997.
Awards and Honors
1993 Award for Scientific Progress of Shanghai city (Study on the relationship between the deficiency of glutathione peroxidase and Ke-Shan disease).
1998 Postdoctoral Fellowship from NIH.
1999 Postdoctoral Fellowship from NIH.
Research
Yan Xu: main area of research interests are bioinformatics and systems biology application in pulmonary research. Our current focus is to systemically identify the critical components in the transcriptional/signaling programs and determine genetic networks regulating lung maturation, surfactant homeostasis, lung cell type specific signaling and asthma associated pathology. We applied systems biology approach that integrates expression profiling with expression-independent data resources including protein interaction, functional annotation, promoter and literature mining to enable the elucidation of genetic networks. Important regulator-target relationships will be selected for experimental validation in vivo and in vitro through collaborations with experimental biologists.
Research Grants and Contracts
Active
5P01HL61646-10 (Weaver) 08/01/04-06/30/09 NIH/NHLBI
Regulation of Respiratory Epithelial Cell Homeostasis
- Project 4: Foxa1 and Foxa2 in Pulmonary Homeostasis (Whitsett)
Role: Co-investigator - Core B: Microarray/Bioinformatics Core (Xu)
Role: PI
5 R01HL085610-03 (Whitsett) 07/10/06-06/30/11 NIH/NHLBI
ABCA3 and Alveolar Homeostasis
Role: Co-investigator
5R01HL090156-02 (Whitsett) 09/28/07-09/30/11 NIH/NHLBI
Transcriptional Control of Respiratory Epithelial Progenior Cells
Role: Co-investigator
1R01HL095589-01 (Whitsett) 04/01/09-03/31/14 NIH/NHLBI
Transcriptional Programming of Asthma Related Pathology in Respiratory Epithelial
Role: Co-investigator
1R01HL086492-01A2(Weaver) 12/01/08-11/30/13 NIH/NHLBI/NIEHS
Role of SFTPC in Pathogenesis of Interstitial Lung Disease
Role: Co-investigator
1R01HL095464-01 (Ikegami) 04/01/09-03/31/14 NIH/NHLBI
Role of C/EBPa in Cytoprotection and Recovery from Lung Injury
Role: Co-investigator
R21 HL 093706 (Bachurski) 4/1/09 to 3/21/11 NIH/NHLBI
Novel Model of Adult Lung Epithelial Stem Cell Expansion
Role: Co-investigator
Completed Research Support
WHITSE00V0 (Whitsett) 03/01/01-02/29/04
Cystic Fibrosis Foundation Therapeutics, Inc
Role: Co-investigator
R457-CR02 (Karp) 09/01/92-8/31/07
Cystic Fibrosis Foundation (CFF) Development Grant, Component II, Bioinformatics Core (Xu )
To develop gene therapy for cystic fibrosis
Role: PI of Informatics Core
R01HL63329-06 (Ikegami) 08/01/03-07/31/07
Role of Surfactant Protein D in Surfactant Homeostasis
Role: Co-investigator
5R01 HL075770-02 (Whitsett) 09/30/03-08/31/07
SHH and Alveolar Formation
Role: Co-investigator
5R01HL38859-18 (Whitsett) 04/01/03-3/31/08
Perinatal Expression of Surfactant Protein Gene SP-B
Role: Co-investigator
2HL050046-12 (Glasser) 04/01/04-03/31/08
Role of SP-C in Familial Interstitial Lung Disease
Role: Co-investigator
Publications, Most Recent
Besnard V, Wert SE, Stahlman MT, Postle AD, Xu Y, Ikegami M, et al. Deletion of Scap in Alveolar Type II Cells Influences Lung Lipid Homeostasis and Identifies a Compensatory Role for Pulmonary Lipofibroblasts. J Biol Chem. 2009 Feb 6;284(6):4018-30.
Wan H, Luo F, Wert SE, Zhang L, Xu Y, Ikegami M, et al. Kruppel-like factor 5 is required for perinatal lung morphogenesis and function. Development (Cambridge, England). 2008 Aug;135(15):2563-72.
Glasser SW, Senft AP, Whitsett JA, Maxfield MD, Ross GF, Richardson TR, et al. Macrophage dysfunction and susceptibility to pulmonary Pseudomonas aeruginosa infection in surfactant protein C-deficient mice. J Immunol. 2008 Jul 1;181(1):621-8.
Dong M, Bridges JP, Apsley K, Xu Y, Weaver TE. ERdj4 and ERdj5 are required for endoplasmic reticulum-associated protein degradation of misfolded surfactant protein C. Mol Biol Cell. 2008 Jun;19(6):2620-30.
Matsuzaki Y, Besnard V, Clark JC, Xu Y, Wert SE, Ikegami M, et al. STAT3 regulates ABCA3 expression and influences lamellar body formation in alveolar type II cells. Am J Respir Cell Mol Biol. 2008 May;38(5):551-8.
Lin S, Ikegami M, Xu Y, Bosserhoff AK, Malkinson AM, Shannon JM. Misexpression of MIA disrupts lung morphogenesis and causes neonatal death. Dev Biol. 2008 Apr 15;316(2):441-55.
Besnard V, Xu Y, Whitsett JA. Sterol response element binding protein and thyroid transcription factor-1 (Nkx2.1) regulate Abca3 gene expression. Am J Physiol Lung Cell Mol Physiol. 2007 Dec;293(6):L1395-405.
Xu Y, Ikegami M, Wang Y, Matsuzaki Y, Whitsett JA. Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells. BMC Genomics. 2007;8:455.
Metzger DE, Xu Y, Shannon JM. Elf5 is an epithelium-specific, fibroblast growth factor-sensitive transcription factor in the embryonic lung. Dev Dyn. 2007 May;236(5):1175-92.
Stahlman MT, Besnard V, Wert SE, Weaver TE, Dingle S, Xu Y, et al. Expression of ABCA3 in developing lung and other tissues. J Histochem Cytochem. 2007 Jan;55(1):71-83.
Dave V, Childs T, Xu Y, Ikegami M, Besnard V, Maeda Y, et al. Calcineurin/Nfat signaling is required for perinatal lung maturation and function. The Journal of clinical investigation. 2006 Oct;116(10):2597-609.
Matsuzaki Y, Xu Y, Ikegami M, Besnard V, Park KS, Hull WM, et al. Stat3 is required for cytoprotection of the respiratory epithelium during adenoviral infection. J Immunol. 2006 Jul 1;177(1):527-37.
Xu Y, Liu C, Clark JC, Whitsett JA. Functional genomic responses to cystic fibrosis transmembrane conductance regulator (CFTR) and CFTR(delta508) in the lung. J Biol Chem. 2006 Apr 21;281(16):11279-91.
Martis PC, Whitsett JA, Xu Y, Perl AK, Wan H, Ikegami M. C/EBPalpha is required for lung maturation at birth. Development (Cambridge, England). 2006 Mar;133(6):1155-64.
Bridges JP, Xu Y, Na CL, Wong HR, Weaver TE. Adaptation and increased susceptibility to infection associated with constitutive expression of misfolded SP-C. J Cell Biol. 2006 Jan 30;172(3):395-407.
Mucenski ML, Nation JM, Thitoff AR, Besnard V, Xu Y, Wert SE, et al. Beta-catenin regulates differentiation of respiratory epithelial cells in vivo. Am J Physiol Lung Cell Mol Physiol. 2005 Dec;289(6):L971-9.
Wan H, Dingle S, Xu Y, Besnard V, Kaestner KH, Ang SL, et al. Compensatory roles of Foxa1 and Foxa2 during lung morphogenesis. J Biol Chem. 2005 Apr 8;280(14):13809-16.
Whitsett JA, Wert SE, Xu Y. Genetic disorders of surfactant homeostasis. Biol Neonate. 2005;87(4):283-7.
Wan H, Xu Y, Ikegami M, Stahlman MT, Kaestner KH, Ang SL, et al. Foxa2 is required for transition to air breathing at birth. Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14449-54.
Miller LA, Wert SE, Clark JC, Xu Y, Perl AK, Whitsett JA. Role of Sonic hedgehog in patterning of tracheal-bronchial cartilage and the peripheral lung. Dev Dyn. 2004 Sep;231(1):57-71.
Whitsett JA, Bachurski CJ, Barnes KC, Bunn PAJ, Case LM, Cook DN, et al. Functional genomics of lung disease. Second annual Pittsburgh International Lung Conference, October 2003. Am J Respir Cell Mol Biol. 2004 Aug;31(2 Suppl):S1-81.
Karp CL, Flick LM, Park KW, Softic S, Greer TM, Keledjian R, et al. Defective lipoxin-mediated anti-inflammatory activity in the cystic fibrosis airway. Nat Immunol. 2004 Apr;5(4):388-92.
Lian X, Yan C, Yang L, Xu Y, Du H. Lysosomal acid lipase deficiency causes respiratory inflammation and destruction in the lung. Am J Physiol Lung Cell Mol Physiol. 2004 Apr;286(4):L801-7.
DeFelice M, Silberschmidt D, DiLauro R, Xu Y, Wert SE, Weaver TE, et al. TTF-1 phosphorylation is required for peripheral lung morphogenesis, perinatal survival, and tissue-specific gene expression. J Biol Chem. 2003 Sep 12;278(37):35574-83.
Xu Y, Clark JC, Aronow BJ, Dey CR, Liu C, Wooldridge JL, et al. Transcriptional adaptation to cystic fibrosis transmembrane conductance regulator deficiency. J Biol Chem. 2003 Feb 28;278(9):7674-82.
Xu Y, Demarest K, Hitzemann R, Sikela JM. Gene coding variant in Cas1 between the C57BL/6J and DBA/2J inbred mouse strains: linkage to a QTL for ethanol-induced locomotor activation. Alcohol Clin Exp Res. 2002 Jan;26(1):1-7.
Ehringer MA, Thompson J, Conroy O, Xu Y, Yang F, Canniff J, et al. High-throughput sequence identification of gene coding variants within alcohol-related QTLs. Mamm Genome. 2001 Aug;12(8):657-63.
Xu Y, Ehringer M, Yang F, Sikela JM. Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization. Alcohol Clin Exp Res. 2001 Jun;25(6):810-8.
Xu Y, Kakhniashvili DA, Gremse DA, Wood DO, Mayor JA, Walters DE, et al. The yeast mitochondrial citrate transport protein. Probing the roles of cysteines, Arg(181), and Arg(189) in transporter function. J Biol Chem. 2000 Mar 10;275(10):7117-24.
Professional Organization Memberships
American Thoracic Society
Intelligent Systems for Molecular Biology (ISMB)
The International Society For Computational Biology
Bioinformatics Organization, Inc. (Bioinformatics.org)
Related Areas
This person works in these other areas at Cincinnati Children's Hospital Medical
Center:
