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Paul Allen, PhD

Paul Allen, PhD

Robert L. Kroc Professor, Pathology & Immunology
Chief, Division of Immunobiology


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  • BS: University of Michigan (1974)
  • MS: University of Michigan (1977)
  • PhD: University of Michigan (1981)

Research Interests

The fate and function of T cells is mediated by the T cell receptor (TCR) recognizing a peptide/MHC complex on the surface of an antigen presenting cell. This critical recognition event is highly specific, but paradoxically relatively low affinity. The research in our laboratory is centered upon elucidating how the TCR recognizes antigen, and its relationship to the development and function of T cells. There are three major focus areas: the Hb(64-76)/I-Ek antigen system, a murine model of rheumatoid arthritis, and alloreactivity.

We have developed and extensively characterized a model antigen system based on the Hb(64-76)/I-Ek epitope. This system includes TCR transgenic mice, a series of ligands with defined affinities, transgenic mice expressing the ligands as neo-self antigens, and crystal structures. From studies using these reagents we have been able to define kinetic thresholds for T cell development and tolerance in the thymus and explored the function of the co-receptor molecule, CD4. Using the Hb(64-76)/I-Ek, we have also visualized and quantified the formation of the immunological synapse, a critical structure formed between a T cell and an APC. Using a novel yeast display system, we are now performing directed evolution of TCRs, making them higher affinity and/or with changed specificity, and then determining what functional, structural, and biophysical changes have occurred. Our studies with the Hb(64-76)/I-Ek will provide new insights into how the fascinating TCR recognizes antigen.

The immune system is normally tolerant to self-antigens; however, failure to do so can result in autoimmunity. We utilize a murine model of rheumatoid arthritis (K/BxN) in which transgenic CD4 T cells provide help to B cells in the generation of autoantibodies against glucose 6-phosphate isomerse (GPI)resulting in an inflammatory process similar to human rheumatoid arthritis. The inflammation is joint specific disease, despite GPI being a ubiquitously expressed self protein. Using micro positron emission tomography (microPET), we have visualized and quantified the trafficking of the autoantibodies in the initiation of arthritis. We have shown that the antibodies within 7 minutes specifically localized to the affected joints. We have further delineated the stages involved in the development of arthritis, showing that the localization depended upon mast cells, neutrophils, Fc Receptors, immune complexes, but not C5. We are now investigating how the GPI autoantigen is localized to the joints, and what products of the neutrophils and mast cells are essential for disease induction. To study B cell tolerance in this model, we have recently generated anti-GPI IgG transgenic mice. Using these mice, we will investigate the mechanism of tolerance induction of anti-GPI B cells in non-autoimmune mice and how this tolerance breaks down in pre-arthritic and arthritic K/BxN mice. To investigate the lack of complete T cell tolerance, we have overexpressed an agoinst ligand, and prevented arthritis and anti-GPI antibodies from developing. Unexpectedly, the mice developed systemic autoimmunity, due to the elimination of Treg cells, highlighting one mechanism by which autoreactive T cells are kept in check. Our future studies will continue to explore the role of the adaptive immune system and the innate immune system with the goal of understanding how an autoimmune disease develops and how we can prevent/ ameliorate the disease.

Alloreactivity is the ability of a T cell to recognize foreign MHC molecules, to which the T cell had never been exposed, and is observed in vivo as graft rejection, graft versus host disease, and in vitro by a mixed lymphocyte reaction (MLR). The phenomenon of alloreactivity has been known for a long time; however, the precise molecular basis for it is yet to be fully defined. Previous studies from our laboratory on the peptide specificity of two class II alloresponses have revealed one T cell, where the recognition is degenerate compared to the syngeneic response. Conversely, for a second allo TCR, the allogeneic peptide recognition is as specific as the syngeneic recognition. Thus, these two responses are on opposite ends of the peptide specificity spectrum, making it difficult to make any strong conclusions about the specificity of allorecognition. We are investigating the peptide specificity of the anti-I-Ep alloresponses, using naturally presented self-peptides in a series of unprimed alloreactive T cells and a gain of function approach using a yeast display system in which we will create TCRs which have acquired I-Ep alloreactivity. From these studies, we ascertain what changes in a TCR are required to make it alloreactive and what changes in peptide specificity have occurred. We will then study these alloresponses biophysically and by x-ray crystallography. These studies will allow us to compare and contrast the recognition of a syngeneic and an allogenic ligand by the same TCR. These studies will provide key insights into the molecular basis for the degenerate/specific peptide recognition and significantly contribute to a furthering of our understanding of the molecular basis of alloreactivity.

Editorial Responsibilities

2000 – present Associate Editor Immunity
1995 – 2003 Advisory Editor The Journal of Experimental Medicine
1991 – 1993 Section Editor The Journal of Immunology
1987 – 1991 Associate Editor The Journal of Immunology
1979 – 2000 Editor Immunity

Service to the Department

2003 Р2006  Director, Immunology Program

DBBS Graduate Program Affiliation

  • Immunology Program


Pub Med Search

Shih FF, Racz J, Allen PM. Differential MHC class II presentation of a pathogenic autoantigen during health and disease. J Immunol 176:3438-48, 2006 Abstract
Norian LA, Allen PM. No intrinsic deficiencies in CD8+ T cell-mediated anti-tumor immunity with aging. J Immunol 173:835-844, 2004 Abstract
Wipke BT, Wang Z, Nagengast W, Reichert DE, Allen PM. Staging the initiation of autoantibody induced arthritis: a critical role for immune complexes. J Immunol 172:7694-7702, 2004 Abstract
Hanson HL, Kang SS, Norian LA, Matsui K, O’Mara LA, Allen PM. CD4-directed peptide vaccination augments an antitumor response, but efficacy is limited by the number of CD8+ T cell precursors.. J Immunol 172:4215-4224, 2004 Abstract
Shih FF, Mandik-Nayak L, Wipke BT, Allen PM. Massive thymic deletion results in systemic autoimmunity through elimination of CD4+CD25+ T regulatory cells. J Exp Med 199:323-335, 2004 Abstract
Mandik-Nayak L, Wipke BT, Shih FF, Unanue ER, Allen PM. Despite ubiquitous autoantigen expression, arthritogenic autoantibody response initiates in the local lymph node. Proc Natl Acad Sci USA 99:14368-14373, 2002 Abstract
Hailman E, Burack WR, Shaw AS, Dustin ML, Allen PM. Immature CD4+CD8+ thymocytes form a multifocal immunological synapse with sustained tyrosine phosphorylation. Immunity 16:839-848, 2002 Abstract
Basu D, Horvath S, O’Mara L, Donermeyer D, Allen PM. Two MHC surface amino acid differences distinguish foreign peptide recognition from autoantigen specificity. J Immunol 166:4005-4011, 2001 Abstract
Kersh GJ. Miley MJ, Nelson CA, Grakoui A, Horvath S, Donermeyer DL, Kappler J, Allen PM, and Fremont. Structural and functional consequences of altering a peptide MHC anchor residue. J Immunol 164:5788-5796, 2001 Abstract
Basu D, Horvath S, Matsumoto I, Fremont DH, Allen PM. Molecular basis for recognition of an arthritic peptide and a foreign epitope on distinct MHC molecules by a single TCR. J Immunol 164:5788-5796, 2000 Abstract
Grakoui A, Bromley SK, Sumen C, Davis MM, Shaw AS, Allen PM, Dustin ML. The immunological synapse: A molecular machine controlling T cell activation. Science 285:221-227, 1999 Abstract
Williams CB, Engle DL, Kersh GJ, White JM, Allen PM. A kinetic threshold between negative and positive selection based on the longevity of the T cell receptor-ligand complex. J Exp Med 189:1531-1544, 1999 Abstract
Daniel C, Horvath S, Allen PM. A basis for alloreactivity: MHC helical residues broaden peptide recognition by the TCR. Immunity 8:543-552, 1998 Abstract
Kersh GJ, Kersh EN, Fremont DH, Allen PM. High- and low-potency ligands with similar affinities for the TCR: The importance of kinetics in TCR signaling. Immunity 9:817-826, 1998 Abstract
Kersh EN, Shaw AS, Allen PM. Fidelity of T cell activation through multistep T cell receptor zeta phosphorylation. Science 281:572-575, 1998 Abstract

Lab Phone: 314-747-2046
Office Location: BJC-IH Building, Office Suite C 8417