Igs Expressed by Chronic Lymphocytic Leukemia B Cells Show Limited Binding-Site Structure Variability

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated.

[1]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[2]  A Tramontano,et al.  Antibody modeling: implications for engineering and design. , 2000, Methods.

[3]  N. Chiorazzi,et al.  Production of autoantibodies by CD5-expressing B lymphocytes from patients with chronic lymphocytic leukemia , 1989, The Journal of experimental medicine.

[4]  Robert Sabatier,et al.  IMGT standardized criteria for statistical analysis of immunoglobulin V‐REGION amino acid properties , 2004, Journal of molecular recognition : JMR.

[5]  Xiao-Jie Yan,et al.  From bloodjournal.hematologylibrary.org at PENN STATE UNIVERSITY on February 21, 2013. For personal use only. , 2007 .

[6]  P. Rousseeuw Silhouettes: a graphical aid to the interpretation and validation of cluster analysis , 1987 .

[7]  Nikolaos Laoutaris,et al.  Over 20% of patients with chronic lymphocytic leukemia carry stereotyped receptors: Pathogenetic implications and clinical correlations. , 2006, Blood.

[8]  A Tramontano,et al.  Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the VH domains of immunoglobulins. , 1990, Journal of molecular biology.

[9]  E. Meffre,et al.  Unmutated and mutated chronic lymphocytic leukemias derive from self-reactive B cell precursors despite expressing different antibody reactivity. , 2005, The Journal of clinical investigation.

[10]  A. Lesk,et al.  Standard conformations for the canonical structures of immunoglobulins. , 1997, Journal of molecular biology.

[11]  Steven L. Allen,et al.  Multiple Distinct Sets of Stereotyped Antigen Receptors Indicate a Role for Antigen in Promoting Chronic Lymphocytic Leukemia , 2004, The Journal of experimental medicine.

[12]  Michael R. Anderberg,et al.  Cluster Analysis for Applications , 1973 .

[13]  Anna Tramontano,et al.  A database of immunoglobulins with integrated tools: DIGIT , 2011, Nucleic Acids Res..

[14]  L. Rassenti,et al.  Chronic lymphocytic leukemia B cells express restricted sets of mutated and unmutated antigen receptors. , 1998, The Journal of clinical investigation.

[15]  Guillermo Sapiro,et al.  Shapes of antibody binding sites: qualitative and quantitative analyses based on a geomorphic classification scheme. , 2006, The Journal of organic chemistry.

[16]  T. T. Wu,et al.  AN ANALYSIS OF THE SEQUENCES OF THE VARIABLE REGIONS OF BENCE JONES PROTEINS AND MYELOMA LIGHT CHAINS AND THEIR IMPLICATIONS FOR ANTIBODY COMPLEMENTARITY , 1970, The Journal of experimental medicine.

[17]  K. Stamatopoulos,et al.  Extensive intraclonal diversification in a subgroup of chronic lymphocytic leukemia patients with stereotyped IGHV4-34 receptors: implications for ongoing interactions with antigen. , 2009, Blood.

[18]  Yang Zhang,et al.  Scoring function for automated assessment of protein structure template quality , 2004, Proteins.

[19]  S. Malek,et al.  Chronic Lymphocytic Leukemia , 2019, Methods in Molecular Biology.

[20]  M. Grever,et al.  National Cancer Institute-sponsored Working Group guidelines for chronic lymphocytic leukemia: revised guidelines for diagnosis and treatment. , 1996, Blood.

[21]  Göran Roos,et al.  Somatically mutated Ig V(H)3-21 genes characterize a new subset of chronic lymphocytic leukemia. , 2002, Blood.

[22]  E. Meffre,et al.  Chronic Lymphocytic Leukemia Cells Recognize Conserved Epitopes Associated with Apoptosis and Oxidation , 2008, Molecular medicine.

[23]  H. Döhner,et al.  Strikingly homologous immunoglobulin gene rearrangements and poor outcome in VH3-21-using chronic lymphocytic leukemia patients independent of geographic origin and mutational status. , 2005, Blood.

[24]  D. Rossi,et al.  Molecular and clinical features of chronic lymphocytic leukaemia with stereotyped B cell receptors: results from an Italian multicentre study , 2009, British journal of haematology.

[25]  P. Labute,et al.  Antibody modeling assessment , 2011, Proteins.

[26]  Paolo Marcatili,et al.  PIGS: automatic prediction of antibody structures , 2008, Bioinform..

[27]  Luca Varani,et al.  Computational Docking of Antibody-Antigen Complexes, Opportunities and Pitfalls Illustrated by Influenza Hemagglutinin , 2011, International journal of molecular sciences.

[28]  Göran Roos,et al.  Subsets with restricted immunoglobulin gene rearrangement features indicate a role for antigen selection in the development of chronic lymphocytic leukemia. , 2004, Blood.

[29]  N. Chiorazzi,et al.  Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. , 1999, Blood.

[30]  Andrew C. R. Martin,et al.  Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen. , 2003, Journal of molecular biology.

[31]  M. Minden,et al.  Chronic lymphocytic leukaemia is driven by antigen-independent cell-autonomous signalling , 2012, Nature.

[32]  A. Lesk,et al.  Canonical structures for the hypervariable regions of immunoglobulins. , 1987, Journal of molecular biology.

[33]  Andrew J. Martin,et al.  Antibody-antigen interactions: contact analysis and binding site topography. , 1996, Journal of molecular biology.

[34]  Kostas Stamatopoulos,et al.  Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies. , 2012, Blood.

[35]  T J Hamblin,et al.  Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia. , 1999, Blood.

[36]  G. Juliusson,et al.  Chronic lymphocytic leukemias utilizing the VH3-21 gene display highly restricted Vlambda2-14 gene use and homologous CDR3s: implicating recognition of a common antigen epitope. , 2003, Blood.

[37]  K. Stamatopoulos,et al.  Evidence for the significant role of immunoglobulin light chains in antigen recognition and selection in chronic lymphocytic leukemia. , 2008, Blood.

[38]  F. Berger,et al.  Over 30% of patients with splenic marginal zone lymphoma express the same immunoglobulin heavy variable gene: ontogenetic implications. , 2012, Leukemia.

[39]  G. Gaidano,et al.  Similarities and Differences Between the Light and Heavy Chain Ig Variable Region Gene Repertoires in Chronic Lymphocytic Leukemia , 2006, Molecular medicine.

[40]  E. Ghia,et al.  Comprehensive characterization of IGHV3-21-expressing B-cell chronic lymphocytic leukemia: an Italian multicenter study. , 2007, Blood.

[41]  Nikolaos Laoutaris,et al.  Stereotyped patterns of somatic hypermutation in subsets of patients with chronic lymphocytic leukemia: implications for the role of antigen selection in leukemogenesis. , 2007, Blood.

[42]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[43]  Anna Tramontano,et al.  Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia. , 2004, The Journal of clinical investigation.

[44]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[45]  A Tramontano,et al.  Conformations of the third hypervariable region in the VH domain of immunoglobulins. , 1998, Journal of molecular biology.

[46]  J. Gribben,et al.  Chronic lymphocytic leukemia B cells of more than 1% of patients express virtually identical immunoglobulins. , 2004, Blood.

[47]  D. Rossi,et al.  Biological and clinical significance of stereotyped B-cell receptors in chronic lymphocytic leukemia , 2010, Haematologica.

[48]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.