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Signaling & Gene Expression in the Immune System

(Cold Spring Harbor Symposia on Quantitative Biology LXIV)

Book Series:  Cold Spring Harbor Symposia on Quantitative Biology
Subject Area(s):  Cell BiologyGeneticsImmunology and Vaccines

Proceedings of 1999 Symposium


© 1999 • 621 pp., illus., color plates, appendices, index
Paper • $115 57.50
ISBN  978-087969570-5
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  •     Description    
  •     Contents    

Description

For the past two decades, much effort has been made to understand the complex interactions between lymphocytes and antigen-presenting cells that result in immune responses. Immunologists have identified an extraordinary diversity of cytokines as players in these interactions, some the products of cellular activation which themselves activate surrounding cells. Meanwhile, another community of investigators, interested in how genes turn on, were using lymphocytes as easily cultivated cells with which to study transcriptional regulation from a molecular perspective. Connections between these areas of study, with their quite different technical vocabularies and experimental approaches, were limited. The 64th Annual Cold Spring Harbor Symposium was therefore a particularly imaginative meeting, intended to provoke a dialogue on the nature of the membrane signals and intracytoplasmic events that provoke the generation of immunity. It did. The debate ranged over biochemistry, physiology, and molecular genetics as well as classical cellular immunology, involving over 70 of the world's leading investigators in a discussion described by the summarizer as the best he had ever attended. The book prompted by the meeting contains personal summaries of the contributions these investigators have made to their fields over the years, with reference to their most recently reported data. This volume therefore contains a remarkably fresh and original perspective on an important aspect of immunology that is necessary to understand in order to undertake rational manipulation of immune responses. All laboratories committed to the future of immunology should have this book, as well as investigators in gene regulation seeking a wide-ranging survey of results achieved with lymphocytes.

Contents

Lymphocyte Development
 
Lymphoid Development from Stem Cells and the Common Lymphocyte Progenitors
(K. Akashi, M. Kondo, S. Cheshier, J. Shizuru, K. Gandy, J. Domen, R. Mebius, D. Traver, and I.L. Weissman)
PU.1: A Shared Transcriptional Regulator of Lymphoid and Myeloid Cell Fates
(H. Singh, R.P. DeKoter, and J.C. Walsh)
Differentiation, Dedifferentiation, and Redifferentiation of B-lineage Lymphocytes: Roles of the Surrogate Light Chain and the Pax-5 Gene
(A. Rolink, S. Nutt, M. Busslinger, E. ten Boekel, T. Seidl, J. Andersson, and F. Melchers)
Notch and the CD4 versus CD8 Lineage Decision
(P. Valdez and E. Robey)
Consequences of Notch-mediated Inhibition of the Transcription Factor E47
(W. Pear, Z. Tang, S. DeRocco, D. Allman, R. Hardy, J. Pui, L. Xu, F. Karnell, J. Aster, and T. Kadesch)
Role of Helix-Loop-Helix Proteins in Lymphocyte Development
(C. Murre)
Controlling Lymphopoiesis with a Combinatorial E-protein Code
(R.J. Barndt and Y. Zhuang)
The Molecular Basis of B Cell Lineage Commitment
(S.L. Nutt, A.G. Rolink, and M. Busslinger)
Role of B-lymphocyte-induced Maturation Protein-1 in Terminal Differentiation of B Cells and Other Cell Lineages
(C. Angelin-Duclos, G. Cattoretti, D. Chang, K.-I. Lin, Y. Lin, J. Yu, and K. Calame)
The Lymphochip: A Specialized cDNA Microarray for the Genomic-scale Analysis of Gene Expression in Normal and Malignant Lymphocytes
(A. Alizadeh, M. Eisen, R.E. Davis, C. Ma, H. Sabet, T. Tran, J.I. Powell, L. Yang, G.E. Marti, D.T. Moore, J.R. Hudson, Jr., W.C. Chan, T. Greiner, D. Weisenburger, J.O. Armitage, I. Lossos, R. Levy, D. Botstein, P.O. Brown, and L.M. Staudt)
Transcription Factors and the Control of Lymphocyte Development
 
Ikaros Chromatin Remodeling Complexes in Control of Differentiation of the Hemo-lymphoid System
(J. Koipally, J. Kim, B. Jones, A. Jackson, N. Avitahl, S. Winandy, M. Trevisan, A. Nichogiannopoulou, C. Kelley, and K. Georgopoulos)
Mechanisms of Transcriptional Regulation in Lymphocyte Progenitors: Insight from an Analysis of the Terminal Transferase Promoter
(P. Ernst, K. Hahm, B.S. Cobb, K.E. Brown, L.A. Trinh, A.S. McCarty, M. Merkenschlager, C.A. Klug, A.G. Fisher, and S.T. Smale)
Mechanisms of mu Enhancer Regulation in B Lymphocytes
(B.S. Nikolajczyk, W. Dang, and R. Sen)
Differential Regulation of Immunoglobulin Gene Transcription via Nuclear Matrix-associated Regions
(C. Webb, R.-T. Zong, D. Lin, Z. Wang, M. Kaplan, Y. Paulin, E. Smith, L. Probst, J. Bryant, A. Goldstein, R. Scheuermann, and P. Tucker)
B-cell-specific Coactivator OCA-B: Biochemical Aspects, Role in B-Cell Development and Beyond
(Y. Luo and R.G. Roeder)
Control of Lymphocyte Differentiation by the LEF-1/TCF Family of Transcription Factors
(T. Reya, R. Okamura, and R. Grosschedl)
Activation and Repression of Wingless/Wnt Target Genes by the TCF/Lef-1 Family of Transcription Factors
(H.C. Korswagen and H.C. Clevers)
The INF- beta Enhancer: A Paradigm for Understanding Activation and Repression of Inducible Gene Expression
(N. Munshi, J. Yie, M. Merika, K. Senger, S. Lomvardas, T. Agalioti, and D. Thanos)
Recombination and Allelic Exclusion
 
V(D)J Recombination: Links to Transposition and Double-strand Break Repair
(M. Gellert, J.E. Hesse, K. Hiom, M. Melek, M. Modesti, T.T. Paull, D.A. Ramsden, and D.C. van Gent)
Non-homologous End-joining Proteins Are Required for V(D)J Recombination, Normal Growth, and Neurogenesis
(J.M. Sekiguchi, Y. Gao, Y. Gu, K. Frank, Y. Sun, J. Chaudhuri, C. Zhu, H.-L. Cheng, J. Manis, D. Ferguson, L. Davidson, M.E. Greenberg, and F.W. Alt)
Regulation of Chromatin Accessibility for V(D)J Recombination
(C. Hernandez-Munain, M.Taylor McMurry, and M.S. Krangel)
What Prevents Intermolecular V(D)J Recombination?
(L.E. Huye, J.-O. Han, and D.B. Roth)
Demethylation and the Establishment of kappa Allelic Exclusion
(R. Mostoslavsky, A. Kirillov, Y.-H. Ji, M. Goldmit, M. Holzmann, T. Wirth, H. Cedar, Y. Bergman)
RAG Expression in B Cells in Secondary Lymphoid Tissues
(W. Yu, H. Nagaoka, Z. Misulovin, E. Meffre, H. Suh, M. Jankovic, N. Yannoutsos, R. Casellas, E. Besmer, F. Papavasiliou, X. Qin, and M.C. Nussenzweig)
Antibody Diversification and Selection in the Mature B-Cell Compartment
(M.S. Neuberger, A. Lanoue, M.R. Ehrenstein, F.D. Batista, J.E. Sale,and G.T. Williams)
Molecular Mechanism of Immunoglobulin Class Switch Recombination
(K. Kinoshita, C.-G. Lee, J. Tashiro, M. Muramatsu, X.-C. Chen, K. Yoshikawa, and T. Honjo)
Molecular Aspects of Somatic Hypermutation of Immunoglobulin Genes
(U. Storb, A. Peters, N. Kim, H.M. Shen, G. Bozek, N. Michael, J. Hackett, Jr., E. Klotz, J.D. Reynolds, L.A. Loeb, and T.E. Martin)
T-cell Activation and Receptor Signaling
 
Structural, Biochemical, and Biophysical Studies of HLA-A2/Altered Peptide Ligands Binding to Viral-peptide-specific Human T-cell Receptors
(B.M. Baker, Y.-H. Ding, D.N. Garboczi, W.E. Biddison, and D.C. Wiley)
Visualizing T-cell Recognition
(M.M. Davis, C. Wülfing, M.F. Krummel, P.A. Savage, J. Xu, C. Sumen, M.L. Dustin, and Y.-H. Chien)
Three Signals and a Master Switch in the Regulation of T-cell Immunity
(A. Lanzavecchia)
Studies on the Adaptor Molecule LAT
(L.E. Samelson, S.C. Bunnell, R.P. Trible, T. Yamazaki, and W. Zhang)
The Adaptor Proteins LAT and SLP-76 Are Required for T-cell Activation
(T.S. Finco, D. Yablonski, J. Lin, and A. Weiss)
Signaling in Primary Thymocytes after Presentation of Altered Peptide Ligands by Antigen-presenting Cells or MHC-peptide Tetramers
(L.A. Smyth, L. Reynolds, R. Tyrrell, O. Williams, T. Norton, T. Schumacher, V. Tybulewicz, S.C. Ley, and D. Kioussis)
The Impact of Pre-T Cell Receptor Signals on Gene Expression in Developing T Cells
(H. von Boehmer, I. Aifantis, O. Azogui, C. SaintRuf, and F. Grassi)
The PTK-STAT Signaling Pathway Has Essential Roles in T-cell Activation in Response to Antigen Stimulation
(T. Welte, D. Leitenberg, B.N. Dittel, B.K. al-Ramadi, W.R. Hansen, B. Xie, C.A. Janeway, Jr., A.L.M. Bothwell, K. Bottomly, and X.-Y. Fu)
CTLA-4—The Costimulatory Molecule That Doesn't: Regulation of T-cell Responses by Inhibition
(C.A. Chambers and J.P. Allison)
B-cell Activation and Receptor Signaling
 
Mechanisms of Self-tolerance and Autoimmunity: From Whole-animal henotypes to Molecular Pathways
(C.C. Goodnow, R. Glynne, D. Mack, B. Weintraub, J. Rathmell, J.I. Healy, S. Chaudhry, L. Miosge, A. Loy, and L. Wilson)
The Maintenance and the Activation Signal of the B-cell Antigen Receptor
(M. Reth and J. Wienands)
Inhibitory Receptors and Their Modes of Action
(D.C. Fong and J.C. Cambier)
Cell Death and Survival in the Immune System
 
Genetic Analysis of Apoptotic and Survival Signals
(T.W. Mak and W.-C. Yeh)
Death and Survival Signals Determine Active/Inactive Conformations of Pro-apoptotic BAX, BAD, and BID Molecules
(S.J. Korsmeyer, A. Gross, H. Harada, J. Zha, K. Wang, X.-M. Yin, M. Wei, and S. Zinkel)
Control of Apoptosis in Hematopoietic Cells by the Bcl-2 Family of Proteins
(J.M. Adams, D.C.S. Huang, H. Puthalakath, P. Bouillet, G. Vairo, K. Moriishi, G. Hausmann, L. O'Reilly, K. Newton, S. Ogilvy, M.L. Bath, C.G. Print, A.W. Harris, A. Strasser, and S. Cory)
RIPs: An Emerging Family of Kinases Involved in Pro-inflammatory and Apoptotic Signaling
(V.M. Dixit)
Receptor-mediated Apoptosis in T Lymphocytes
(J. Zhang, A. DeYoung, H.G. Kasler, N.H. Kabra, A.A. Kuang, G. Diehl, S.J. Sohn, C. Bishop, and A. Winoto)
Role of the Nuclear Hormone Receptor ROR gamma in Transcriptional Regulation, Thymocyte Survival, and Lymphoid Organogenesis
(D.R. Littman, Z. Sun, D. Unutmaz, M.J. Sunshine, H.T. Petrie, and Y.-R. Zou)
What Keeps a Resting T Cell Alive?
(C.B. Thompson, J.C. Rathmell, K.A. Frauwirth, T. Lindsten, C.M. Rudin, J. Opferman, P. Ashton-Rickardt, M.H. Harris, N.S. Chandel, P.T. Schumacker, and M.G. Vander Heiden)
Cytokine Signaling and Responses
 
Differential Roles of Cytokine Signaling during T-cell Development
(R. Moriggl, J.-C. Marine, D.J. Topham, S. Teglund, V. Sexl, C. McKay, R. Piekorz, D. Wang, E. Parganas, A. Yoshimura, and J.N. Ihle)
Negative Regulation of Cytokine Signaling by the SOCS Proteins
(N.A. Nicola, S. Nicholson, D. Metcalf, J.-G. Zhang, M. Baca, A. Farley, T.A. Willson, R. Starr, W. Alexander, and D.J. Hilton)
IL-4 Signaling Is Regulated through the Recruitment of Phosphatases, Kinases, and SOCS Proteins to the Receptor Complex
(J. Losman, X.P. Chen, H. Jiang, P.-Y. Pan, M. Kashiwada, C. Giallourakis, S. Cowan, K. Foltenyi, and P. Rothman)
Signaling via the IL-2 and IL-7 Receptors from the Membrane to the Nucleus
(W.J. Leonard, K. Imada, H. Nakajima, A. Puel, E. Soldaini, and S. John)
Potential Roles of Stat1 and Stat3 in Cellular Transformation
(J.F. Bromberg and J.E. Darnell, Jr.)
Innate Immune Induction of the Adaptive Immune Response
(R. Medzhitov and C.A. Janeway, Jr.)
Attenuation of Tumor Necrosis Factor alpha Gene Transcription in Macrophages by an Autocrine Factor
(M. Baer, S. Nedospasov, and P.F. Johnson)
Mechanisms of Chromatin Recognition and Transcriptional Regulation by LEF-1 and the Wnt/Wg-responsive LEF-1: beta -Catenin Complex
(A. Tutter, G.S. McAlpine, and K.A. Jones)
HIV and SIV Nef Modulate Signal Transduction and Protein Sorting in T Cells
(J. Skowronski, M.E. Greenberg, M. Lock, R. Mariani, S. Salghetti, T. Swigut, and A.J. Iafrate)
Transcription Factor IRF-1 and Its Family Members in the Regulation of Host Defense
(T. Taniguchi, N. Tanaka, K. Ogasawara, S. Taki, M. Sato, and A. Takaoka)
NF- kappa B/NFAT/TRAF
 
NF- kappa B Activation by Tumor Necrosis Factor and Interleukin-1
(Z. Cao, M. Tanaka, C. Regnier, M. Rothe, A. Yamit-hezi, M.E. Fuentes, M.H. Durnin, S.A. Dalrymple, and D.V. Goeddel)
Role of NF- kappa B in T-lymphocyte Development
(R.E. Voll, and S. Ghosh)
The I kappa B Kinase: A Master Regulator of NF- kappa B, Innate Immunity, and Epidermal Differentiation
(M. Delhase and M. Karin)
Signaling through Calcium, Calcineurin and NF-AT in Lymphocyte Activation and Development
(K. Stankunas, I.A. Graef, J.R. Neilson, S.-H. Park, and G.R. Crabtree)
NF-AT5: The NF-AT Family of Transcription Factors Expands in a New Direction
(C. López-Rodríguez, J. Aramburu, A.S. Rakeman, N.G. Copeland, D.J. Gilbert, S. Thomas, C. Disteche, N.A. Jenkins, and A. Rao)
Signal Integration by Transcription-factor Assemblies: Interactions of NFAT1 and AP-1 on the IL-2 Promoter
(L. Chen, A. Rao, and S.C. Harrison)
Structure and Mechanism in NF- kappa B / I kappa B Signaling
(T. Huxford, S. Malek, and G. Ghosh)
Structural Studies of Human TRAF2
(H. Wu, Y.C. Park, H. Ye, and L. Tong)
Structural and Biochemical Analysis of Signal Transduction by the TRAF Family of Adaptor Proteins
(S.M. McWhirter, S.S. Pullen, B.G. Werneburg, M.E. Labadia, R.H. Ingraham, J.J. Crute, M.R. Kehry, and T. Alber)
T-cell Differentiation
 
The Molecular Basis of T-cell Differentiation
(R.A. Flavell, B. Li, C. Dong, H.-T. Lu, D.D. Yang, H. Enslen, C. Tournier, A. Whitmarsh, M. Wysk, D. Conze, M. Rincón, and R.J. Davis)
Tissue-specific Regulation of Cytokine Gene Expression
(I.-C. Ho, J.I. Kim, S.J. Szabo, and L.H. Glimcher)
Bi-stable Transcriptional Circuitry and GATA-3 Auto-activation in Th2 Commitment
(K.M. Murphy, W. Ouyang, S. Ranganath, and T.L. Murphy)
Multiple Levels of Regulation of Th2 Cytokine Gene Expression
(N. Arai, H.J. Lee, I. Ferber, H. Kurata, and A. O'Garra)
Bias in the Expression of IL-4 Alleles: The Use of T Cells from a GFP Knock-in Mouse
(C. Pannetier, J. Hu-Li, and W.E. Paul)
Summary: Signals and Beyond
(R.A. Flavell)
Author Index
Subject Index