Structural Basis for Clonal Diversity of the Public T Cell Response to Dominant Epitopes from Cytomegalovirus and Influenza

Title of Thesis: STRUCTURAL BASIS FOR CLONAL DIVERSITY OF THE PUBLIC T CELL RESPONSE TO DOMINANT EPITOPES FROM CYTOMEGALOVIRUS AND INFLUENZA Xinbo Yang, Doctor of Philosophy, 2016 Thesis Directed By: Professor Roy A. Mariuzza Department of Cell Biology and Molecular Genetics A diverse T cell receptor (TCR) repertoire is a prerequisite for effective viral clearance. However, knowledge of human TCR repertoire to defined viral antigens is limited. Recent advances in high-throughput sequencing (HTS) and single-cell sorting have revolutionized the study of human TCR repertoires to different types of viruses. In collaboration with the laboratory of Dr. Nan-ping Weng (National Institute on Aging, NIH), we applied unique molecular identifier (UMI)-labelled HTS, single-cell paired TCR analysis, surface plasmon resonance, and X-ray crystallography to exhaustively interrogate CD8+ TCR repertoires specific for cytomegalovirus (CMV) and influenza A (Flu) in HLA-A2+ humans. Our two CMV-specific TCR-pMHC structures and two Flu-specific TCR-pMHC structures provide a plausible explanation for the much higher diversity of CMV-specific than Flu-specific TCR repertoires in humans. Our comprehensive biochemical and structural portrait of two different anti-viral T cell responses may contribute to the future development of predictors of immunity or disease at the individual level. STRUCTURAL BASIS FOR CLONAL DIVERSITY OF THE PUBLIC T CELL RESPONSE TO DOMINANT EPITOPES FROM CYTOMEGALOVIRUS AND INFLUENZA

[1]  Y. Naumov,et al.  Narrowing of Human Influenza A Virus-Specific T Cell Receptor α and β Repertoires with Increasing Age , 2015, Journal of Virology.

[2]  Robyn L Stanfield,et al.  How TCRs bind MHCs, peptides, and coreceptors. , 2006, Annual review of immunology.

[3]  X. Jin,et al.  The human cytotoxic T-lymphocyte (CTL) response to cytomegalovirus is dominated by structural protein pp65: frequency, specificity, and T-cell receptor usage of pp65-specific CTL , 1996, Journal of virology.

[4]  E. Metter,et al.  TCRβ repertoire of CD4+ and CD8+ T cells is distinct in richness, distribution, and CDR3 amino acid composition , 2016, Journal of leukocyte biology.

[5]  M. Diamond,et al.  Antibody Response to Hypervariable Region 1 Interferes with Broadly Neutralizing Antibodies to Hepatitis C Virus , 2015, Journal of Virology.

[6]  W. Paul,et al.  Differentiation of effector CD4 T cell populations (*). , 2010, Annual review of immunology.

[7]  Mark M. Davis,et al.  Deconstructing the Peptide-MHC Specificity of T Cell Recognition , 2014, Cell.

[8]  Michael J. Bevan,et al.  CD8+ T Cells: Foot Soldiers of the Immune System , 2011, Immunity.

[9]  M. A. Saper,et al.  Structure of the human class I histocompatibility antigen, HLA-A2 , 1987, Nature.

[10]  C. Carlson,et al.  Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire , 2010, Science Translational Medicine.

[11]  M. Zambon,et al.  Influenza A antigen exposure selects dominant Vbeta17+ TCR in human CD8+ cytotoxic T cell responses. , 2001, International immunology.

[12]  M. Lefranc.  IMGT, the International ImMunoGeneTics Information System. , 2011, Cold Spring Harbor protocols.

[13]  R. Zamoyska,et al.  T cell receptor signalling networks: branched, diversified and bounded , 2013, Nature Reviews Immunology.

[14]  James McCluskey,et al.  A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity. , 2003, Immunity.

[15]  R. Purcell,et al.  Neutralizing antibodies to hepatitis C virus (HCV) in immune globulins derived from anti-HCV-positive plasma. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Thomas S. Watkins,et al.  Naive CD8+ T-cell precursors display structured TCR repertoires and composite antigen-driven selection dynamics , 2015, Immunology and cell biology.

[17]  D. Wiley,et al.  Antigenic peptide binding by class I and class II histocompatibility proteins. , 1994, Structure.

[18]  David I Stuart,et al.  A structural basis for immunodominant human T cell receptor recognition , 2003, Nature Immunology.

[19]  James McCluskey,et al.  T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex , 2015, Nature Immunology.

[20]  R. E. Tillman,et al.  Regulation of T‐cell receptor β‐chain gene assembly by recombination signals: the beyond 12/23 restriction , 2004, Immunological reviews.

[21]  Nicholas A Williamson,et al.  A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule , 2007, Nature Immunology.

[22]  Andrew K. Sewell,et al.  Human TCR-Binding Affinity is Governed by MHC Class Restriction1 , 2007, The Journal of Immunology.

[23]  Mikhail Shugay,et al.  Towards error-free profiling of immune repertoires , 2014, Nature Methods.

[24]  D. Price,et al.  The molecular basis for public T-cell responses? , 2008, Nature Reviews Immunology.

[25]  Marc Bonneville,et al.  Structural Bases for the Affinity-Driven Selection of a Public TCR against a Dominant Human Cytomegalovirus Epitope1 , 2009, The Journal of Immunology.

[26]  B M Baker,et al.  Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical. , 1999, Immunity.

[27]  P. Swanson.  The bounty of RAGs: recombination signal complexes and reaction outcomes , 2004, Immunological reviews.

[28]  Brian M. Baker,et al.  The basis for limited specificity and MHC restriction in a T cell receptor interface , 2013, Nature Communications.

[29]  B. Nag,et al.  Refolding and reconstitution of functionally active complexes of human leukocyte antigen DR2 and myelin basic protein peptide from recombinant alpha and beta polypeptide chains. , 1995, The Journal of biological chemistry.

[30]  A. McMichael,et al.  Cytotoxic T lymphocytes recognize a fragment of influenza virus matrix protein in association with HLA-A2 , 1987, Nature.

[31]  Meir Glick,et al.  Stable, soluble T-cell receptor molecules for crystallization and therapeutics. , 2003, Protein engineering.

[32]  James McCluskey,et al.  T cell antigen receptor recognition of antigen-presenting molecules. , 2015, Annual review of immunology.

[33]  K. Kedzierska,et al.  Recognition of Distinct Cross-Reactive Virus-Specific CD8+ T Cells Reveals a Unique TCR Signature in a Clinical Setting , 2014, The Journal of Immunology.

[34]  I. Messaoudi,et al.  The many important facets of T-cell repertoire diversity , 2004, Nature Reviews Immunology.

[35]  P. Griffiths,et al.  The pathogenesis of human cytomegalovirus , 2015, The Journal of pathology.

[36]  Richard A. Olshen,et al.  Diversity and clonal selection in the human T-cell repertoire , 2014, Proceedings of the National Academy of Sciences.

[37]  M. Bonneville,et al.  Selection of T Cell Clones Expressing High-Affinity Public TCRs within Human Cytomegalovirus-Specific CD8 T Cell Responses1 , 2005, The Journal of Immunology.

[38]  A. Singer,et al.  αβ T cell receptors that do not undergo major histocompatibility complex-specific thymic selection possess antibody-like recognition specificities. , 2012, Immunity.

[39]  H. Wolfson,et al.  Shape complementarity at protein–protein interfaces , 1994, Biopolymers.

[40]  M. A. Saper,et al.  The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens , 1987, Nature.

[41]  D. Wiley,et al.  HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[42]  P. Doherty,et al.  Wang Antibody Levels in Human Cytomegalovirus Infection Diversity Inversely Correlates with Pathogen-Specific βα T Cell Receptor , 2012 .

[43]  D. Fremont,et al.  Structures of an MHC Class II Molecule with Covalently Bound Single Peptides , 1996, Science.

[44]  Brian G. Pierce,et al.  Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope* , 2015, The Journal of Biological Chemistry.

[45]  D. Price,et al.  A Single Autoimmune T Cell Receptor Recognizes More Than a Million Different Peptides* , 2011, The Journal of Biological Chemistry.

[46]  R. Mariuzza,et al.  Structural basis for the binding of an immunodominant peptide from myelin basic protein in different registers by two HLA-DR2 proteins. , 2000, Journal of molecular biology.

[47]  S. Turner,et al.  T cell mediated immunity to influenza: mechanisms of viral control. , 2014, Trends in immunology.

[48]  P. Moss,et al.  Characterization of human cytomegalovirus peptide-specific CD8(+) T-cell repertoire diversity following in vitro restimulation by antigen-pulsed dendritic cells. , 2002, Blood.

[49]  D. Wiley,et al.  The antigenic identity of peptide-MHC complexes: A comparison of the conformations of five viral peptides presented by HLA-A2 , 1993, Cell.

[50]  R Crowther,et al.  Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures. , 2000, Journal of medicinal chemistry.

[51]  D. Kranz,et al.  Binding properties and solubility of single-chain T cell receptors expressed in E. coli. , 1996, Molecular immunology.

[52]  J. Bell,et al.  Human HLA-A0201-restricted cytotoxic T lymphocyte recognition of influenza A is dominated by T cells bearing the V beta 17 gene segment , 1995, The Journal of experimental medicine.

[53]  Robyn L. Stanfield,et al.  An αβ T Cell Receptor Structure at 2.5 Å and Its Orientation in the TCR-MHC Complex , 1996, Science.

[54]  M. Oettinger,et al.  RAG: a recombinase diversified , 2009, Nature Immunology.