Patrick Swanson, Ph.D.
Appointment(s) and Titles:
Associate Professor of Medical Microbiology and Immunology
Associate Professor of Medicine
Director, Flow Cytometry Core Facility (see http://www.creighton.edu/cytometry/)
Education:
B.S. 1990, Chemistry, St. Olaf College, Northfield, Minnesota
Ph.D. 1995, Chemistry, University of Michigan, Ann Arbor, Michigan
Post-Doctoral Fellow, 1995-1999, Molecular Biology and Genetics, The Johns Hopkins University, Baltimore, Maryland
Research Interests:
I am generally interested in mechanisms of immune repertoire diversification. My research program is currently focused on studying various aspects of V(D)J recombination, the process by which immunoglobulin and T cell receptor genes are assembled during lymphocyte development. V(D)J recombination is initiated by the RAG1 and RAG2 proteins, which together introduce DNA breaks in the antigen receptor loci, which are subsequently repaired by components of the non-homologous DNA end-joining (NHEJ) repair pathway (Fig. 1). The laboratory has two major ongoing projects. The first project is primarily biochemical, and is broadly aimed at identifying and characterizing protein-DNA complexes involved in cleavage and repair phases of V(D)J recombination. We are particularly interested in learning how the DNA ends produced by RAG cleavage are transferred to the NHEJ apparatus for repair. We believe NHEJ is facilitated by the associated of NHEJ factors with pre-cleavage RAG complexes, as we have recently published evidence for the association of the Ku70/Ku80 with full-length RAG1. The second project involves determining whether enforced expression of catalytically inactive RAG1 in mice can impair secondary V(D)J recombination events triggered by engagement of self-antigen (receptor editing) or in response to immunization (receptor revision), and whether defects in these processes increase susceptibility to malignancy or autoimmune disease. These research projects are or have been supported by both intramural and extramural grants, including grants awarded by the National Institutes of Health and the American Cancer Society.
Selected Publications:
Swanson PC. The DDE motif in RAG-1 is contributed in trans to a single active site that catalyzes the nicking and transesterification steps of V(D)J recombination. Mol. Cell. Biol. 2001; 21:449-458.
Swanson PC. Fine structure and activity of discrete RAG-HMG complexes on V(D)J recombination signals. Mol. Cell. Biol. 2002; 22:1340-1351.
Swanson PC. A RAG-1/RAG-2 tetramer supports 12/23-regulated synapsis, cleavage and transposition of V(D)J recombination signals. Mol. Cell. Biol. 2002; 22:7790-7801
Swanson PC, Volkmer D. and Wang L. Full-length RAG-2, and not full-length RAG-1, specifically suppresses RAG-mediated transposition, but not hybrid joint formation or disintegration" J. Biol. Chem. 2004; 279:4034-4044.
Raghavan SC, Swanson PC, Wu X, Hsieh C-L, and Lieber MR. "A Non-B DNA Structure at the bcl-2 Major Breakpoint Region is Cleaved by the RAG Complex" Nature 2004; 428:29-31.
Swanson PC "The bounty of RAGs: recombination signal complexes and reaction outcomes" Immunol. Rev. 2004; 200:90-114.
Raghavan, SC, Swanson, PC, Ma Y, and Lieber MR. "Double-strand break formation by the RAG complex at the Bcl-2 major breakpoint region and at other non-B DNA structures in vitro" Mol. Cell. Biol. 2005; 25:5904-19.
Bergeron S, Madathiparambil T, Swanson PC. "Both HMG-boxes and the acidic tail of HMGB1 regulate RAG-mediated recombination signal synapsis and cleavage in vitro." J Biol Chem. 2005; 280:31314-31324.
Bergeron S, Anderson DK, Swanson PC. "RAG and HMGB1 proteins: Purification and biochemical analysis of recombination signal complexes." Methods Enzymol. 2006; 408:511-528.
Kriatchko AN, Anderson DK, and Swanson PC. " Identification and characterization of a gain-of-function RAG-1 mutant." Mol. Cell. Biol. 2006; 26:4712-4728.
Raghavan SC, Gu J, Swanson PC, and Lieber MR. "The structure-specific nicking of small heteroduplexes by the RAG complex: Implications for lymphoid chromosomal translocations." DNA Repair 2007; 6:751-759. PMID: 17307402
Ciubotaru M, Kriatchko AN, Swanson PC, Bright FV, and Schatz DG. Fluorescence resonance energy transfer analysis of RSS configuration in the RAG1/2 synaptic complex. Mol Cell Biol. 2007; 27:4745-4758. PMID: 17470556
Zhang M and Swanson PC. V(D)J recombinase binding and cleavage of cryptic recombination signal sequences identified from lymphoid malignancies. J. Biol. Chem. 2008; 11:6717-6727. PMID: 18187418
Raval P, Kriatchko AN, Kumar, S, and Swanson PC. Evidence for Ku70/Ku80 association with full-length RAG1. Nucleic Acids Res. 2008; 36:2060-2072. PMID: 18281312
Kriatchko AN, Bergeron S, and Swanson PC. HMG-box domain stimulation of RAG1/2 cleavage is metal ion dependent. BMC Molecular Biology. 2008; 9:32. PMID: 18380906
Lu H, Shimazaki N, Raval P, Gu J, Watanabe G, Schwarz K, Swanson PC, and Lieber MR. A biochemically defined system for coding joint formation in V(D)J recombination. Mol Cell. 2008; 31:485-497. PMID: 18722175