The Genitourinary Developmental Molecular Anatomy Project
Total Page:16
File Type:pdf, Size:1020Kb
SPECIAL ARTICLE www.jasn.org GUDMAP: The Genitourinary Developmental Molecular Anatomy Project Andrew P. McMahon,* Bruce J. Aronow,† Duncan R. Davidson,‡ Jamie A. Davies,§ ʈ Kevin W. Gaido, Sean Grimmond,¶ James L. Lessard,** Melissa H. Little,¶ S. Steven Potter,** Elizabeth L. Wilder,†† and Pumin Zhang,‡‡ for the GUDMAP project *Department of Molecular and Cellular Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts; †Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio; ‡Medical Research Council Human Genetics Unit, Western ʈ General Hospital, and §Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom; Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina; ¶Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia; **Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio; ††Renal and Urogenital Development, Kidney Injury and Repair, and Basic Science of Cystic Kidney Disease Research, National Institutes of Health Roadmap Interdisciplinary Research Working Group, Bethesda, Maryland; and ‡‡Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas ABSTRACT toward the treatment of disease have In late 2004, an International Consortium of research groups were charged with the task thrown a spotlight on the normal develop- of producing a high-quality molecular anatomy of the developing mammalian urogenital mental programs that orchestrate develop- tract (UGT). Given the importance of these organ systems for human health and repro- ment of our organ systems. Which cells duction, the need for a systematic molecular and cellular description of their developmen- make up an organ? How are they gener- tal programs was deemed a high priority. The information obtained through this initiative ated? Which factors control these events in is anticipated to enable the highest level of basic and clinical research grounded on a time and space, ensuring a co-herent, func- 21st-century view of the developing anatomy. There are three components to the Geni- tional system? How are organs repaired? tourinary Developmental Molecular Anatomy Project GUDMAP; all of these are intended What controls the numbers of any given to provide resources that support research on the kidney and UGT. The first provides cell type and the overall balance of cell ontology of the cell types during UGT development and the molecular hallmarks of those number in the organ? Addressing any of cells as discerned by a variety of procedures, including in situ hybridization, transcriptional these pertinent and fascinating questions profiling, and immunostaining. The second generates novel mouse strains. In these strains, requires a solid foundation in develop- cell types of particular interest within an organ are labeled through the introduction of a mental anatomy. The overarching goal of specific marker into the context of a gene that exhibits appropriate cell type or structure- the Genitourinary Developmental Molec- specific expression. In addition, the targeting construct enables genetic manipulation ular Anatomy Project (GUDMAP) initia- within the cell of interest in many of the strains. Finally, the information is annotated, tive is to establish this foundation for the collated, and promptly released at regular intervals, before publication, through a data- UGT. The ensuing data generated by the base that is accessed through a Web portal. Presented here is a brief overview of the initiative will enable, facilitate, and stimu- Genitourinary Developmental Molecular Anatomy Project effort. late research into, and our understanding of, this critical organ network. J Am Soc Nephrol 19: 667–671, 2008. doi: 10.1681/ASN.2007101078 One in nine Americans has chronic kid- velopmental deficiencies likely underlie or Published online ahead of print. Publication date ney disease (CKD), and the same num- influence susceptibility to a range of dis- available at www.jasn.org. ber is at increased risk for developing eases of the urogenital tract (UGT), as well Correspondence: Dr. Andrew P. McMahon, Depart- CKD. Approximately 12% of women in as adversely affecting fertility. One example ment of Molecular and Cellular Biology and Harvard the United States have a problem conceiv- is the link between nephron number, de- Stem Cell Institute, Harvard University, 16, Divinity Ave- ing or bringing a baby to term. Approxi- termined at the outset by a fetal develop- nue, Cambridge, MA 02138. Phone: 617-496-3757; Fax: 617-496-3763; E-mail: [email protected]; mately 3% of all children are born with a mental program, and hypertension and re- consortium Web address: http://www.gudmap.org recognized birth defect. Some of the most nal disease later in life.1 E.L.W.’s current affiliation is Office of Portfolio Anal- common are those that affect the genito- This increased realization of a link be- ysis and Strategic Initiatives, National Institutes of urinary system, with cryptorchidism and tween development and disease and the Health, Bethesda, Maryland. hypospadias being the most common male opportunities that might come from ex- Copyright © 2008 by the American Society of birth defect. Furthermore, less obvious de- ploiting our developmental understanding Nephrology J Am Soc Nephrol 19: 667–671, 2008 ISSN : 1046-6673/1904-667 667 SPECIAL ARTICLE www.jasn.org INTRODUCTION TO GUDMAP by the NIDDK and the National Institute of approach to map gene expression do- Child Health and Human Development. mains and identify patterns that are diag- In September 2001, the National Insti- nostic of specific anatomic regions or in- tute of Diabetes and Digestive and Kid- dividual cell types. WISH has been used ney Diseases (NIDDK) was advised by a AN ANATOMIC ONTOLOGY FOR generally to survey expression of specific working group of its National Advisory THE ANNOTATION OF THE classes of genes within the UGT. Tran- Council to form a strategic plan to con- DEVELOPING UGT scriptional regulators, as a functional sider how stem cells and developmental category, are valuable cell type–specific biology might be used to explore the re- Early discussions among the members of markers in several developmental stud- pair and replacement of damaged organs the consortium highlighted the need to ies.3 Furthermore, their known regula- and to determine how they might pro- develop a high-resolution anatomy- tory actions can provide insights into vide insights into the pathologic pro- based ontology of the UGT. This ontol- possible actions within expressing cells, cesses underlying developmental defects ogy would not only provide a common stimulating further experimental in- and disease. A separate working group of descriptive language for cell types within quiry. Optimizing a WISH procedure for the National Advisory Council high- the developing UGT, an essential prereq- sensitivity, penetration, and specificity, a lighted developmental biology as an un- uisite for any search algorithm and the systematic, genome-scale screen was per- derstudied area of bladder research. logical construction of the critical GUD- formed for the spatial expression of a These reports led the NIDDK to convene MAP database, but also draw these terms majority of mouse transcriptional fac- a panel of advisors in January 2003 to into a developmental series of hierarchi- tors in at embryonic day 15.5 UGT (Yu et discuss approaches that would provide a cal relationships among the cell popula- al. in preparation; http://www.gudma- fundamental description of the develop- tions of the UGT. M.H.L. spearheaded p.org/Research/Protocols/). The anno- ing UGT. the important goal of a high-resolution tated data representing approximately The working group recommended anatomic ontology of the UGT in con- 1500 mouse transcriptional factors can several strategies to reach this goal: (1)A sultation with GUDMAP members, be queried through the GUDMAP data- high-throughput in situ analysis of gene members of the EuReGene network base. In addition, an analysis of the ex- expression in the developing UGT, (2)a (http://www.euregene.org), and other pression pattern of genes classified as ex- high-resolution analysis of a limited set international experts in the field. The on- tracellular on the basis of gene ontology of genes in time and space to define the tology was published in 2007.2 This on- terms and previously described to be ex- emergence of anatomic and functional tology provides a framework for anno- pressed during kidney development has domains, and (3) the creation of a data- tating the expression data. Furthermore, been submitted.4 A second comprehen- base to make these data readily and the expression studies provide an ongo- sive genome-scale screen of mammalian promptly available to the research com- ing test and challenge to the ontology. signals and their receptors is under way, munity. The ontology will inevitably evolve as together with prioritized gene sets based Requests for applications were issued molecular approaches reveal molecularly on spatial expression profiling of the de- in late 2003, and a funded consortium of distinct cell types that are not currently veloping UGT (see below). All data are seven laboratories was formed from the incorporated into histology-based anat- released on a regular basis through the applicants late in 2004. The group con- omy. We urge that this ontology be GUDMAP database.