Diversity and differentiation in the adaptive immune system


T cell receptors (TCRs) and B cell receptors (BCRs) exhibit an astounding amount of diversity. Estimates vary widely, but theoretically, there can be as many as 1025 different receptor combinations. At any given moment, there are likely on the order of 108 different receptors in the human body. 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 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 are 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.

Click here to learn about sequencing the immune repertoire

Somatic recombination, allelic exclusion and clonal expansion

The V(D)J recombination described above involves somatic recombination, which occurs in naïve, inactivated cells. It was previously thought that all receptors produced by an individual B or T cell were identical for that one cell. The term, allelic exclusion, defines the process in which only one copy of a recombined V(D)J-C region is expressed, despite the presence of two copies in every cell. However, there is new evidence that allelic inclusion can also occur, albeit at low proportion, which undermines the previous belief of one recombined receptor to one cell stoichiometry. 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.

B cell maturation  

Following activation and clonal expansion, B cells undergo a maturation process that generally takes place over three steps: 1) isotype switching, 2) somatic hypermutation, and 3) affinity maturation. The order of these steps varies, though, and some cells may skip one or more steps completely.  

Isotype switching  

Isotype switching, also known as class switch recombination, increases the effector function of antibodies secreted by B cells. The heavy chain of antibodies and BCR are classified as different isotypes (IgM, IgD, IgG, IgA, or IgE) and spans both the variable and constant regions. While the variable region recognizes antigens, the tail of the constant region (i.e., fragment crystallizable (Fc) region) interacts with proteins involved in the complement system or cell surface receptors.  

Naïve B cells first express IgM and/or IgD isotypes until activation, which results in a switch to the IgA, IgE, or IgG isotype. Each isotype can induce a different effect on immune response ranging from the induction of antibody-dependent cell-mediated cytotoxicity (ADCC) or antibody-dependent cell-mediated phagocytosis (ACDP), degranulation of mast cells or basophils, and/or activation of the complement system.  

The BCR and antibody isotype is determined by the combination of different signals obtained from activation of the BCR, coreceptors (e.g., CD40), cytokine receptors, and toll-like receptors (TLR). These signals will activate the activation-induced cytidine deaminase (AID) enzyme to induce mismatch mutations followed by double-stranded breaks. These breaks are repaired by non-homologous end joining (NHEJ) in “switch regions” of the heavy chain. The constant region of the heavy chain is comprised of different CH exons that are each preceded by a switch region and intronic promoter. Depending on the signals that activate AID, specific CH exons will be excised, and the remaining combination of CH exons will determine the BCR isotype.  

In summary, isotype switching allows for different immune effector functions against the same target antigen. Because the isotype class is determined by the constant region, it is important to use an immune sequencing technology that spans from the highly variable CDR3 region into the constant region for a more complete analysis of B cell antigen binding and isotype switching. 

Somatic hypermutation and affinity maturation 

Somatic hypermutation and affinity maturation 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