Chapter 59: Adaptive Immunity: Lymphocyte Antigen Receptors

The innate immune system is often capable of containing and eradicating microbial invaders, but some microbes have evolved ways to subvert or evade innate immunity. The next line of host defense is the adaptive immune system, which is composed of lymphocytes (also called lymphoid cells) and their secreted factors (see Table 57–1).

A critical property of adaptive immunity is that the immune response is specifically tailored against different microbes. This is achieved by first generating an enormous number of diverse lymphocytes, each with a unique antigen specificity. Before they see their antigen, these lymphocytes are called naïve (Figure 59–1). How these cells function is closely linked to how they develop from stem cells, so in order to understand how lymphocytes can aid host defense or can cause disease, it is first necessary to understand lymphocyte development.

As described in Chapter 58, all white and red blood cells originate from stem cells in the fetal liver and yolk sac during embryonic life and in the bone marrow after birth (see Figure 58–1). The common lymphoid progenitor is a type of stem cell that gives rise to lymphocytes of the adaptive immune system, including B cells and T cells. The common lymphoid progenitor is also the source of innate lymphocytes, such as natural killer (NK) cells. The process by which common lymphoid progenitors develop into lymphocytes depends on cytokines, and mutations in the genes encoding the receptors of these cytokines are often the cause of severe combined immunodeficiency, a complete absence of mature lymphocytes (see Chapter 68).

The ratio of T cells to B cells is approximately 3:1. Figure 59–1 describes the origin of B cells and two of the main types of T cells. Often T cells are named by markers we can detect on their cell surface, called “cluster of differentiation” (CD) markers: helper T cells are CD4-positive (CD4+), whereas cytotoxic T cells are CD8-positive (CD8+). Table 59–1 compares various important features of B cells and T cells. These features will be discussed in detail in this and later chapters.

All vertebrates produce enormously diverse pools of antigen receptors; in humans, this pool is estimated to comprise 100 million different specificities, protecting us from millions of potential pathogens. How do we accomplish this with a genome that only contains approximately 20,000 genes? The solution is that during their development, T and B lymphocytes do something extremely unconventional. They switch on a program of DNA rearrangement, cutting their DNA, removing pieces, and shuffling other pieces, to form entirely new coding sequences in their antigen receptor genes. The two most important enzymes in this process are recombinases, called RAG-1 and RAG-2 (recombination-activating genes). The RAG genes have been found in our first vertebrate ancestors from 500 million years ago.

This DNA rearrangement is absolutely necessary for our adaptive immune system; mutations in these RAG genes halt the development of lymphocytes and result in severe combined immunodeficiency (see Chapter 68). However, DNA rearrangement is also risky. The RAG proteins are supposed to work only in specific locations (i.e., in the immunoglobulin and T-cell receptor gene loci, as discussed below), but errors do occur. If the recombinase makes a rearrangement with the wrong gene, it could kill the cell, or worse, it could cause it to divide uncontrollably, resulting in a leukemia or lymphoma.

First, we will discuss the development of B cells, which detect antigen with their immunoglobulins, and then we will discuss T cells, which detect antigen with their T-cell receptors (TCR).

B cells perform two important functions: (1) they differentiate into plasma cells that produce antibodies (also called immunoglobulins) and (2) they can become long-lived memory B cells that can rapidly respond to a reinfection. The immunoglobulin on the B-cell surface is its antigen receptor (B-cell receptor or BCR) and the ability of a B-cell precursor to make this antigen receptor determines whether it is allowed to develop into a mature B cell.

B-cell precursors first arise from stem cells in the fetal liver, but by the time of birth, these stem cells migrate to the bone marrow, which is their main location during childhood and adult life. Unlike T cells, B cells do not require the thymus for maturation.

The maturation of B cells has two phases: the first is the antigen-independent phase, which consists of stem cells, pre-B cells, and B cells, and it is during this phase that the B cell recombines its immunoglobulin genes to make a unique antigen receptor. For pre-B cells to differentiate into B cells, a functional immunoglobulin must be present on the cell surface. A protein called Bruton’s tyrosine kinase (BTK) detects this immunoglobulin and signals to the cell to continue to divide and differentiate. A mutation in the gene encoding this protein causes X-linked agammaglobulinemia, a condition in which cells cannot progress to the pre-B cell stage and no antibodies are made (see Chapter 68).

During the second phase, which is the antigen-dependent phase, mature B cells with functional antigen receptors interact with antigens. This phase will be covered in more detail in Chapter 61.

The immunoglobulin (Ig), or BCR, of a mature B cell is an IgM molecule with an additional region at the end of its heavy chain that tethers it to the B-cell surface. Approximately 10⁹ B cells are produced each day, but only a small fraction of these make it from the bone marrow into the circulation, and unless they are activated through their antigen receptors, circulating B cells have a short life span (i.e., days or weeks). In this chapter, we will explore the structure and diversity of BCRs, and in Chapter 61, we will describe how these antigen receptors cause activation of B cells and how the resulting antibodies provide host defense.

Antibody Structure

Antibodies are glycoproteins made up of light (L) and heavy (H) polypeptide chains. The terms light and heavy refer to molecular weight; light chains have a molecular weight of about 25,000, whereas heavy chains have a molecular weight of 50,000 to 70,000. The simplest antibody molecule has a Y shape (Figure 59–2) and consists of four polypeptide chains: two identical H chains and two identical L chains. In other words, even though you received copies of H and L chain genes from each of your parents, each B cell ultimately synthesizes only one of the H chain genes and one of the L chain genes to use to form an antibody, and therefore, all of the subsequent antibodies from that B cell and its progeny use the same H and L chains. Table 59–2 is a summary of the properties of the human lymphocyte antigen receptors.

One end of the Y is composed of two identical pieces that bind the antigen, and therefore, this is called the antigen-binding fragment (or Fab). The Fab includes the variable region of the L chain (V_L) and the variable region of the H chain (V_H), as well as the constant region of the L chain (C_L) and the first constant region of the H chains (C_H1). The portions of the L and H chains that actually bind the antigen are only 5 to 10 amino acids long, each composed of three extremely variable (hypervariable) amino acid sequences. Antigen–antibody binding involves electrostatic and van der Waals’ forces and hydrogen and hydrophobic bonds rather than covalent bonds. The remarkable specificity of antibodies is due to these hypervariable regions.

The other end of the Y is a single stalk, where the H chains come together, and it is made of the remaining three or four constant regions of each of the H chains (C_H2, etc.). This is called the constant or “crystallizable” fragment (or Fc). You might think that the Fab is the most important part of the antibody because it binds the antigen, but the Fc is needed to attach the antibody to host cells (e.g., via Fc receptors) or to complement (at the C_H2 domain). The Fc is also the region that is used to fuse IgM and IgA together into larger “multimers.” It is also necessary for transport of IgA across epithelial barriers and transport of IgG from mother to fetus through the placenta.

There are five classes of antibodies: IgM, IgD, IgG, IgE, and IgA. Each class has structural differences that make it unique. For example, IgG and IgA have three C_H domains, whereas IgM and IgE have four. The structural differences between the antibody classes translate into important functional differences. Mature naïve B cells start out making only IgM and IgD but later “switch” to making the other classes. We will discuss the different antibody functions and how the B cells class-switch in Chapter 61.

L chains can be of two types, κ (kappa) or λ (lambda), which differ in their constant regions. Either type can pair with H chains in all classes of immunoglobulins (IgG, IgM, etc.), but once a B cell chooses to use κ or λ, it shuts off the other L chain gene, so that all of the immunoglobulin from any one B cell contains only one type of L chain. In humans, the ratio of immunoglobulins containing κ chains to those containing λ chains is approximately 2:1, and a value dramatically different can be a sign of a monoclonal immunoglobulin-producing malignancy such as multiple myeloma.

H chains are distinct for each of the five immunoglobulin classes and are designated γ (gamma), α (alpha), μ (mu), ε (epsilon), and δ (delta). The V_H hypervariable region of the H chain joins with V_L in binding antigen; the opposite regions of the V_H chains form the Fc fragment, which determines which class the antibody is and, therefore, what its biologic activities will be (see Chapter 61).

Antibody Genes

As described earlier, each antibody is composed of four immunoglobulin chains (two light chains and two heavy chains). There are two light chain gene clusters, one encoding kappa light chain (κL), on human chromosome 2, and one encoding lambda light chain (λL), on chromosome 22. All heavy chain genes (μH, δH, γH, εH, and αH) are together in a cluster on chromosome 14. The heavy chains and light chains are assembled after recombining gene segments within their respective gene clusters, a process that is directed by recombinase enzymes (RAG1 and RAG2). A schematic diagram of gene recombination is shown in Figure 59–3.

First, the V_H and V_L genes are recombined. Each cluster contains dozens of different V gene segments widely separated from the D (diversity, seen only in H chains), J (joining), and C gene segments. The V_H region of each heavy chain is encoded by three gene segments (V + D + J). In the synthesis of a heavy chain, one particular V region (out of ~45) is translocated to lie close to one particular D segment (out of ~23), one particular J segment (out of 6), and one C segment.

The V_H/C_H combination is transcribed together on an RNA molecule and spliced to produce an mRNA that codes for the complete heavy chain, encoded by a single V, D, and J segment attached to a C segment. Why are IgM and IgD the first antibodies that are produced? The newly assembled V + D + J gene segments are closest to the Cμ and Cδ genes! In Chapter 61, we will describe how class switching leads to IgG, IgE, and IgA, which are further downstream in the heavy chain locus.

The V_L region of each L chain is encoded by two gene segments (V + J). In the assembly of an L chain, the same process occurs except that there are slightly fewer possible V segments (~30–35 in kappa and lambda), and neither of the L chains have D segments. Also, the kappa chain gene has a single Cκ, whereas the lambda chain gene has four Cλ segments, one already associated with each J segment. The L chain comes from a similar translocation in which a single V and J are brought close together and then transcribed and translated with the appropriate C segment. Note that the DNA of the unused V, D, and J genes is discarded; once a particular B cell has recombined its light and heavy chains, it is committed to making antibody with only one specificity.

The H and L chains are synthesized as separate peptides and then folded and assembled in the cytoplasm by means of disulfide bonds to form H2L2 units. Finally, an oligosaccharide is added to the constant region of the heavy chain, and the BCR molecule is transported to the cell surface.

Clonal Selection

Note that the genetic recombination outlined earlier can lead to an enormous number of possible combinations. There are approximately 10¹¹ possible heavy chain–light chain combinations! Antibody diversity depends on (1) multiple gene segments, (2) their rearrangement into different sequences, (3) the combining of different L and H chains in the assembly of immunoglobulin molecules, and (4) mutations. A fifth mechanism called junctional diversity applies primarily to the antibody heavy chain. Junctional diversity occurs by the addition of new nucleotides at the splice junctions between the V-D and D-J gene segments. The resulting antibodies have the potential to recognize the three-dimensional structure of a wide range of proteins, carbohydrates, nucleic acids, and lipids.

Despite the enormous potential diversity, the actual specificities represented among the pool of circulating B cells that we each have is somewhat smaller (about 10⁶). Each immunologically responsive B cell bears copies of a single BCR on its surface (initially composed of its VDJ + Cμ or Cδ, paired with a VJ + Cκ or VJ + Cλ chain) that can react with one antigen (or closely related group of antigens). Even after that B cell divides, all of its progenies, or clones, will continue to make antibodies with the same antigen specificity.

There are two steps by which B-cell precursors are “auditioned” and selected to be available to become activated antibody-producing plasma cells. (This process is similar to that of T-cell clonal selection, described later in this chapter and in Figure 59–6, but selection of B cells occurs in the bone marrow rather than in the thymus.) The first step of B-cell clonal selection is called positive selection. Pre-B cells lack surface BCR. If a B-cell precursor fails to rearrange its immunoglobulin gene segments and generate a functional BCR, it dies before it reaches the mature B-cell stage. This is called positive selection because only those cells that do generate a BCR are allowed to survive and mature. For example, mutations in the genes encoding the recombinase enzymes (see above) result in a failure to generate antigen receptors and therefore a deficiency of lymphocytes (severe combined immunodeficiency).

Similarly, a mutation in the gene on the X chromosome that encodes BTK, which is important for transmitting the BCR signal from the cell surface, results in the disease X-linked agammaglobulinemia, in which B cells and antibodies are absent. These patients are more susceptible to bacterial infections in their sinuses, lungs, and gastrointestinal tract because they lack the antibodies that usually protect these barrier surfaces (see Chapter 68).

Pre-B cells that do successfully generate surface IgM pass through positive selection and progress to become B cells. At this stage, their IgM BCRs immediately encounter self-antigens. Remember that, whereas TCRs can only bind peptides complexed with major histocompatibility complex (MHC) proteins, the BCR can potentially bind to any circulating proteins, lipids, carbohydrates, or nucleic acids. However, because this phase of development occurs in the bone marrow rather than in the peripheral tissues or secondary lymphoid organs, all of the antigens that the B cell could encounter at this stage are self-antigens. During this phase, called negative selection, if the BCR strongly binds a self-antigen, this indicates high potential for autoreactivity.

This cell will be removed from the pool of mature B-cell clones, although it has one chance to escape this fate by a process called receptor editing. In this process, an alternate V_L combination using an unused light chain allele can replace the previous allele, creating a new IgM receptor. But if this receptor is also autoreactive, the B cells are either killed by apoptosis or rendered “anergic” (their production of surface IgM is turned off and they become insensitive to activation). It is estimated that 25% to 50% of circulating B cells have undergone receptor editing. This phase is called negative selection because it ensures that only B cells that do not strongly bind self-antigens are allowed to leave the bone marrow and, therefore, will be self-tolerant.

Class Switching

Initially, all B cells that exit the bone marrow carry IgM specific for antigen. At this stage, they may be considered mature, because they have a functional BCR, but naïve, because they have not yet encountered their cognate antigen. Later, in a process called class switching, further gene rearrangement enables new antibodies that use the same V_H but different C_H chains. (In Chapter 61, we will describe how activation of B cells causes this class switching and the function of the different Ig classes.) A B cell that has class switched from IgM can never go back.

Allelic Exclusion

A single B cell has one maternal and one paternal copy of the L chain genes (both κ and λ) and the H chain gene. As described earlier, B cells that recognize self-antigens during clonal selection can attempt “receptor editing,” swapping in the alternate allele, to escape apoptosis or anergy. But once they have succeeded in exiting the bone marrow as a mature B cell, the alleles that gave them the successful BCR are fixed and the others are silenced. This is called allelic exclusion. We all have a diverse mixture of B-cell clones expressing different combinations of paternal and maternal genes. The precise mechanism of how the alternate alleles are turned off is unknown.

Like B cells, T-cell precursors derive from common lymphoid progenitors. But unlike B cells, T-cell development includes a step in which the precursors migrate through a specialized organ called the thymus, which is why they are abbreviated “T” cells. Note that prior to entering the thymus, T-cell precursors lack antigen receptors (TCRs) and lack the other surface receptors that support TCR signaling. It is during passage through the thymus that a T-cell precursor begins to express a unique TCR, and upon exiting the thymus, they are called mature naïve T cells because at this stage they have never seen foreign antigens.

Note that the thymus begins to degenerate at the time of puberty, yet adults continue to produce new T cells, suggesting that another site might take over once the thymus stops functioning. Nevertheless, it is clear that the thymus is required for normal development of T cells, as patients with a congenital disease called DiGeorge’s syndrome, who are born without a thymus, are T-cell deficient and die at an early age of infection if they are not treated (see Chapter 68).

T-Cell Receptor Structure

Earlier, we described BCRs as having two identical light chains (lambda or kappa) and two identical heavy chains (mu, delta, gamma, alpha, or epsilon). TCRs have analogous chains but only have two chains instead of four. With rare exceptions, which we will discuss later in the chapter, the TCR is composed of a single α (alpha) chain and a single β (beta) chain (Figure 59–4 and Table 59–2). Each chain includes a variable region, which includes the hypervariable region that binds to the peptide–MHC complex, and a constant region, which attaches the α chain and β chain to each other.

The α chain and β chain are mostly located outside the cell, and they are fixed to the cell membrane by a transmembrane domain and a short cytoplasmic tail. The tail binds to a molecule called CD3ζ (CD3-zeta). Although it is not actually part of the antigen receptor, all T cells have CD3 proteins in association with TCR. The purpose of CD3 is to transmit the TCR peptide recognition signal from the surface to the inside of the cell. This is achieved through intracellular tyrosine kinases that are bound to CD3 and phosphorylate downstream second messengers.

The CD4 and CD8 proteins are coreceptors for the TCR; they sit in the T-cell membrane and bind to nonpolymorphic regions on MHC (class II and class I, respectively). The cytoplasmic domains of CD4 and CD8 amplify the TCR signal transmission, also through a cytoplasmic tyrosine kinase (see Chapter 60).

T-Cell Receptor Genes

During their passage through the thymus cortex, each double-positive T-cell precursor synthesizes a different, highly specific TCR. Rearrangement of variable, diversity, and joining gene segments, analogous to those that encode the B-cell immunoglobulin receptor, accounts for the remarkable ability of T cells to recognize millions of different antigens.

The TCR genes are first expressed by double-negative thymocytes, starting with recombination of the β chain. The TCR β chain gene is located on human chromosome 7, and, like the heavy chain genes of immunoglobulins, it is composed of V, D, and J segments that are selected and joined at random through a process that requires the recombinase enzymes (RAG1 and RAG2). One of approximately 48 Vβ segments, one of two Dβ segments, and one of approximately 13 Jβ segments are randomly selected and translocated next to one another, followed by translocation close to one of two Cβ segments. The new V + D + J + Cβ gene is then transcribed, and its mRNA is spliced and translated into a functional TCR β chain (Figure 59–5).

A similar process occurs to recombine the TCR α chain locus, although, like the light chain genes of BCRs, the α chain gene of the TCR has no “D” regions. The α chain is therefore constructed by translocating one of approximately 45 Vα segments (selected at random) adjacent to one of approximately 50 Jα segments (also selected at random), a process that also requires RAG recombination. (Unlike the BCR light chain genes, which occur at two separate κ and λ loci, there is only one TCR α chain gene locus, on human chromosome 14.) Next, the randomly assembled V + J segments are translocated close to a Cα region, and after splicing the resulting mRNA, the TCR α chain protein is synthesized.

As occurs in B cells during V(D)J recombination, when the RAG proteins recombine the DNA of the TCR α and β chain gene loci, the unused pieces of DNA are permanently excised, with their ends joined together to form rings. These rings of DNA are called T-cell receptor excision circles (or TRECs), and they are easily detected using a polymerase chain reaction (PCR) assay that amplifies them in the blood of people with normal T-cell development.

In fact, many public health departments in the United States now use this assay in all newborns as a screening test for T-cell deficiency; because over 70% of T cells generate TRECs as a byproduct of their TCR, the absence of these TRECs prompts further testing to find out why a baby’s T cells are failing to reach this stage. This test is highly cost-effective because detecting T-cell deficiency at the time of birth allows doctors to anticipate immunodeficiency and prepare for a stem cell transplant before the baby has severe infectious complications (see Chapter 68).

Positive and Negative Thymic Selection

Exactly analogous to B-cell development, each individual-cell precursor in the thymus has a unique TCR, and even after it divides, its progeny, or clones, will carry an identical TCR. Because of the large number of Vα and Vβ segments, including those that come from the paternal and maternal copies of the α and β chain genes, TCR recombination can theoretically generate 10¹³ different receptor combinations! But we only have around 10⁷ T cells in our bodies. Before they can exit the thymus, T-cell precursors are subjected to thymic selection, a rigorous two-step “audition,” analogous to that described earlier for B cells, that generates functional T cells ready to identify and respond to foreign antigen (Figure 59–6):

1. First, double-positive cells in the thymus cortex migrate past specialized thymus cells bearing MHC proteins and presenting “self”-peptides. T-cell precursors, which lack both CD4 and CD8, begin to express both proteins and recombine their TCR genes to generate unique TCRs. If these “double-positive” cells bind to the MHC proteins they encounter, they are given a necessary survival signal through their newly formed TCR, leading them to divide into a population of clones (see Figure 59–6A). This is called positive selection, because only the T-cell precursors that do bind to MHC are chosen to survive. (The self-peptides presented at this stage serve as a proxy for the diversity of peptides that the mature T cells will encounter when they leave the thymus.)

   Cells that fail this step can make further attempts; because all cells have maternal and paternal alleles of their TCR genes, a T cell stuck at this stage can continue to mutate and re-audition TCR genes to make a more suitable MHC-binding receptor. However, most double-positive cells do not survive positive selection. In addition, the type of MHC that is bound by the TCR during positive selection will determine which type of single-positive T cell will develop; for example, if the cell binds strongly to class II MHC, then it turns off CD8 expression and remains (single) CD4-positive, and the opposite is true if the cell binds class I MHC. (This is sometimes referred to as “the rule of eight” because CD4-positive cells bind to class II MHC [4 × 2 = 8], and CD8-positive cells bind to class I MHC [8 × 1 = 8]).

   Why is this important? For a T cell to function, it is essential that its TCR can interact strongly with an appropriate MHC molecule, and positive selection guarantees that the T cells that eventually exit the thymus have functional MHC-binding TCRs.

2. There is a second selection process that occurs as double-positive cells that have survived positive selection begin to move to the thymus medulla. As described earlier, these cells are continuing to contact thymus cells that display self-antigens complexed with class I MHC or class II MHC. Any T cell that binds too strongly to these self-presenting cells is deleted by a process of programmed cell death, or apoptosis (see Figure 59–6B). This is called negative selection, because only the T cells that do not strongly bind to self-peptides are allowed to survive. For negative selection to be efficient, the thymic cells must display a wide repertoire of self-peptides. A transcription factor called the autoimmune regulator (AIRE) directs this array of self-peptides in the thymus.

   Why is this important? The removal of self-reactive cells ensures that the naïve T cells that eventually exit the thymus are not specific for self-antigens, and this self-tolerance is one of the key ways the immune system discriminates between what is self and what is foreign.

   Thymic selection uses a tightly controlled signal threshold that ensures TCR binding to self MHC is strong (positive selection) and TCR binding to self antigens is weak (negative selection). Stated another way, if TCR binding to self MHC is too weak, those cells are deleted and if TCR binding to self antigens is too strong, those cells are deleted. The end result is a naïve T cells that binds well to self MHC and not well to self antigen but well to foreign antigen such as microbial antigens. Mutations in genes that control TCR signaling or in the gene encoding AIRE can cause autoimmune disease due to defective thymic selection (see Chapter 66).

In summary, positive and negative selection remove all but the T-cell clones that react weakly with self-peptides presented in complexes with MHC proteins. Note that the same MHC proteins that are required for initial thymic selection of T-cell precursors later become the critical signals for activating T cells through their TCRs.

Approximately 95% of the body’s T cells are CD4-positive or CD8-positive cells that carry αβ TCRs, as described earlier. These cells have a highly diverse TCR repertoire, capable of responding to a wide range of potential infectious agents. A few other T cells develop in an unusual manner: although they still pass through the thymus, they have a highly restricted TCR repertoire, capable of responding quickly but to a narrow range of antigens. Therefore, because these cells respond more rapidly and are less diverse than other T cells, they are often called “innate-like” (see Table 59–2).

One type of innate-like T cell is the NK-T cell. As their name implies, NK-T cells share many features with innate NK cells, including surface receptors and markers that are important for NK cell function (see Chapter 58). But do not confuse the two cell types! NK-T cells are not innate cells; they have an αβ T-cell receptor and require the thymus for their development.

The best-described NK-T cell, called the “invariant” NK-T (iNKT) cell, uses a highly limited set of V, D, and J gene segments to create the α and β receptor chains of its TCR (see Table 59–2). Instead of recognizing peptides complexed with MHC, the TCRs of iNKT cells recognize lipids and glycolipids complexed with an alternate antigen presentation molecule called CD1d. The precise role of NK-T cells is unknown, but they may be important in host defense against organisms that contain certain lipids or in responding to situations of host tissue stress in which lipids are released from damaged cells.

Another unusual T cell is the mucosal-associated invariant T (MAIT) cell. Like NK-T cells, MAIT cells develop in the thymus and use a limited set of α and β gene segments in their TCRs, but they are restricted to a different antigen presentation molecule called MR1 (see Table 59–2). Like class I MHC, MR1 is expressed on a large variety of cells. However, rather than only presenting peptides, MR1 activates MAIT cells with a wide range of other types of antigens. Not all of the ligands bound by MR1 that activate MAIT cell have been identified, but at least some of them are small-molecule metabolites produced by bacteria. This may explain why MAIT cells populate peripheral barrier surfaces, such as the lung, intestine, and liver, where bacterial products are often encountered.

Finally, the gamma-delta (γδ) T cell is perhaps the most unusual innate-like T cell in that it does not have an αβ TCR. Instead, for reasons that are not well understood, at the time when thymic T-cell precursors begin to recombine the α and β chain genes, γδ T cells instead recombine the γ and δ chain genes (located on human chromosomes 7 and 14, respectively). The γ chain gene is composed of V, D, and J segments (similar to the β chain), and the δ chain gene is composed of V and J segments (similar to the α chain). These alternate TCR chains then combine with CD3ζ on the cell surface.

Little is known about the antigens recognized by γδ TCRs, but some of them may be lipids or microbial products. Also, γδ T cells may respond to these antigens in the absence of the usual antigen-presenting molecules, such as MHC. Like MAIT cells, γδ T cells primarily reside in barrier tissues, such as skin and gut. In the blood of healthy individuals, γδ T cells are rare (<5% of lymphocytes), and although they increase in number in response to infections, such as tuberculosis, Listeria, and malaria, their precise role in host defense in unclear.