Immunoglobulin gene analysis as a tool for investigating human immune responses

Abstract

The human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self-reactive B cells removed. Later antigen-dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of seven other classes depending on the required function. There are many instances in human biology where positive and negative selection forces can act to shape the immunoglobulin repertoire and therefore repertoire analysis can provide useful information on infection control, vaccination efficacy, autoimmune diseases, and cancer. It can also be used to identify antigen-specific sequences that may be of use in therapeutics. The juxtaposition of lymphocyte development and numerical evaluation of immune repertoires has resulted in the growth of a new sub-speciality in immunology where immunologists and computer scientists/physicists collaborate to assess immune repertoires and develop models of immune action.

Keywords: B cell; antibody; human; repertoire.

Figure 1

(a) Variable (V), Diversity (D) and Joining (J) gene segments are arranged in a non‐functional state in the germline. During V(D)J recombination, a V, a D and a J gene segment (just V and J in the case of light chains) are brought together at random. RSS sequences ensure gene segments are recombined in the correct order to form a functional variable region sequence. Blue, orange and purple rectangles represent V, D, and J gene segments, respectively, with gray leader regions upstream of the V genes. Turquoise and red triangles represent 12RSS and 23RSS, respectively. Constant region exons are represented by green rectangles. (b) Functional variable regions are composed of four conserved structural framework regions (FR) and three more diverse complementarity determining regions (CDR). The CDR3 regions are the most diverse as they span multiple gene segments and contain random nucleotide addition. C) The CDR loops make the most contact with antigen (PDB ID: 1FVC)

Figure 2

Ig gene repertoire variation between individuals, classes of antibody, and IGHV gene families. (a) Individual variability in a human vaccine response. Average clonality of selected IGHV genes in the repertoire of 12 individuals (each is color coded) at day 7 after challenge with influenza and pneumococcal vaccines.156 Average clonality is the number of sequences divided by the number of clonal families for each individual genes. Average clonality of 1 indicates lack of clonal expansion. (b) PCA analysis of CDR3 physicochemical properties, as defined by kidera factors, showing the difference between Ig genes of IgG1 vs IgG2 subclasses. Data from Martin et al73 (c) Segregation of IGHV family genes by CDR‐H3 physicochemical properties. Minkowsky distance clustering by Brepertoire146 on IgM sequences from B cells in early development in 12 different individuals.76 Each sample is a separate individual. IGHV genes color coded: Yellow; IGHV2, Red;IGHV1, Green; IGHV3, Blue; IGHV4, Violet; IGHV5, Gray; IGHV6