Diversity and differentiation in the adaptive immune system

Introduction

T cell receptors (TCRs) and B cell receptors (BCRs) exhibit an astounding amount of diversity – roughly 1025 different receptor molecules per adult human. This diversity is born out of just seven different building blocks. Alone, these different components, called chains, could only account for a small amount of diversity: alpha/beta or delta/gamma for T-cells and heavy/kappa or heavy/lambda for B-cells. The key to lymphocyte diversity is in the way the chains are encoded. Each chain is made up of multiple segments, and each segment is encoded by multiple genes. These segments recombine to produce an enormous amount of different of configurations.

For background information about BCRs and TCRs, see our T cell and B cell overview page

The diverse antigen receptors of T and B lymphocytes

Diversity among B cell and T cell receptors is largely produced via V(D)J recombination, which involves the shuffling and joining of the variable, diversity, joining, and constant region (abbreviated V, D, J, and C, respectively) gene segments. To provide a snapshot of the potential for variability provided by these gene segments, their distribution and contribution with respect to BCRs is described below:

  • V: The variable (V) gene segments encode components of the light and heavy chain. There are between 29 and 46 different V-segments that can encode each chain type.
  • D: The diversity (D) gene segments encode heavy chain genes only, and there are 23 different D gene segments per heavy chain type.
  • J: The joining (J) gene segments encode light and heavy chain components via 4-6 different gene segments per chain type.
  • C: The constant (C) gene segments encode light and heavy chain components via 1-9 different segments per chain type.

In individual cells, one of each of the numerous V, D, and J segments is used. This unique combination of segments is what determines the binding specificity and downstream applications of B cell secreted immunoglobulins/antibodies and T cell receptors.

V(D)J recombination takes place in the bone marrow for B cells and in the thymus for T cells during the early stages of cell maturation. For the B cell heavy chain receptors, one D gene segment is joined to one J gene segment. Then, one V gene segment is added to the newly formed DJ complex. In the case of T cells, this D-J joining and then V gene addition occurs for either the beta or delta chain. For B cell light chain receptors, and T cell alpha or gamma chain receptors, one V segment is joined with one J segment and no D gene is present.

For information about how BCR and TCR diversity relates to health, see our page on the immune repertoire and adaptome

Structure and diversity of the variable region

The rearranged V(D)J portion of the receptor, termed the Variable- or V-region, is of great interest as it is responsible for antigen binding and specificity. The V-region consists of framework (FR) and complementarity-determining regions (CDR). When the V(D)J-C is translated into the amino acid sequence, the V-region can be further subdivided into several parts consisting of the leader sequence, FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4, and the C-domains. The C-domain codes for various Constant regions.

The CDR3 is of particular interest because it is the most variable portion of the antigen-binding site, and some studies have indicated that CDR3 is especially associated with antigen-specificity. The CDR3 region spans the V(D)J junction. On either side of the D segment in the CDR3 region are variable “N” regions. The N-regions are generated by deleting a few bases and then adding random sequences and are thus hyper-variable. There are about 350,000 unique CDR3 sequences per person among T cell receptor beta chains alone. Only about half of those CDR3s are shared between individuals.

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Somatic recombination, allelic exclusion and clonal expansion

All receptors produced by an individual B or T cell are identical for that cell. This occurs in part because the V(D)J recombination described above, which involves somatic recombination, happens in naïve, inactivated cells. Additionally, allelic exclusion ensures that only one copy of a recombined V(D)J-C region is expressed, despite the presence of two copies in every cell. In allelic exclusion, successful somatic recombination on one chromosome shuts down rearrangement in the homologous chromosome. When the receptors of a naïve B or T cell recognize an antigen, the cell is activated and then proliferates – a process called clonal expansion. This activation and expansion process is what enables the immune system’s specific, adaptive response.

Class switching, somatic hypermutation, and affinity maturation

After B cells have been activated and undergone clonal expansion, they begin the maturation process. This process generally takes place over three steps, though the order of these steps varies, and some cells may skip one or more steps completely.

The first is step called class switching, which is where a B cell can change the class of antibody it produces. There are five main antibody classes: IgM, IgD, IgG, IgE, and IgA. A fifth class, IgD, also exists; however, it is only present in small quantities, and it is unclear whether it has any significant part in immune defense. IgM is the default antibody class and is produced when a naïve B cell is first activated. As the B cell matures, it can change to one of the other antibody classes by making changes to the constant (C) region DNA. This is important because, though the V(D)J region ­– known as the Fab region for B cells – is what binds to the antigen, it is the C-region that determines how the antibody will function.

The second and third steps work somewhat in conjunction with each other. In somatic hypermutation, the BCR gene locus is randomly mutated to produce additional diversity. These mutations can either increase, decrease, or have no effect on the antigen binding affinity. Generally, those B cells which have increased affinity due to somatic hypermutation proliferate more quickly than those that do not. This process of mutation and proliferation to create a group of B cells with higher binding affinity for their cognate antigen is called affinity maturation.

For information about how BCR and TCR diversity relates to health, see our page on the immune repertoire and adaptome