The essential elements of adaptive immunity and their relevance to cancer immunology

Structure of αβ T-cell receptor

The TCR consists of two polypeptide chains, α and β, that are composed of variable (V) and junction (J) domains for the α chain (VJ) and an additional diversity (D) region for the β chain (VDJ) ( Fig. 7.2 ). These chains result from somatic DNA recombination of germline genes during T-cell development in the thymus. Because gene rearrangement occurs at the somatic level, each T cell expresses thousands of copies of an identical single receptor after the recombination process is complete. This gene rearrangement is driven by recombinase-activating genes ( RAG1 and RAG2 ). The TCR α V locus comprises ∼80 gene segments and ∼60 J gene segments. The TCR β locus contains 52 V gene segments, 13 J gene segments, and 2 D segments. A single constant domain links the αβ TCR chains to signaling components of the CD3 complex that are responsible for initiating the signaling cascade within the T cell. Rearrangement of gene segments continues until the T cell receives a positive signal from self-MHC peptide complexes in the thymus or until the cell dies because of a lack of instructive signal from a successful rearrangement. The consequence of having two interacting chains that are derived from such a tremendous diversity of gene segments is the production of T cells each with a unique, highly specific TCRs capable of productively interacting with only a few MHC–peptide complexes. This notion is reinforced by evaluating crystal structures of the TCR, which show that the V region gene segments are clustered at the N-terminus of both the α and β chains, generating an antigen-binding domain that will contact the MHC–peptide complex.

A critical element in adaptive immunity is the ability to discriminate self-derived antigens from foreign or altered self-antigens. On the one hand, this is achieved with the incredible diversity and specificity of the TCR. However, an excessive T-cell pool is energetically demanding and raises the possibility of responding to self-antigens and the initiation of autoimmunity. One part of this puzzle is solved by survival signals in the thymus only being delivered to T cells whose TCR has an ability to engage the host MHC molecules. Those whose TCRs do not “match” the MHC of the host die by neglect. This process is referred to as positive selection . If the resulting TCR has too high an affinity for MHC-self peptide complexes, the bearing T cell will subsequently undergo activation-induced apoptosis, known as negative selection . ^, This process is required to limit autoreactive T cells from transiting to the periphery. Together, these selection events sculpt the T-cell repertoire such that it is focused on discerning alterations in the proteome of the host cells. Interestingly, some of the first identified tumor antigens were shown to be normal melanocyte proteins, suggesting that the selection process is not absolute.

Structure of the B-cell immunoglobulins

Significant similarities are present in the construction of antibodies and their receptor counterparts to the processes that occur with TCR construction. The BCR is composed of heavy and light chains, which together generate the antigen-binding domain ( Fig. 7.2 ). As with T cells, B-cell development and selection is a function of successful steps in the assembly of antigen receptor genes. Progenitor B cells begin by rearranging the heavy chain locus containing V, D, and J gene segments. D-J recombination occurs first, followed by recombination with V genes, and finally the constant (C) region is added. In humans, the heavy chain locus contains 38 to 46 V gene segments, 23 D gene segments, 6 J segments, and 9 C segments. Two light chains, k and l, are available to pair with the heavy chain, and each of these has a high number (∼29–38) of V genes and 5 J genes but no D genes. As with the TCR, this diversity results in a tremendous number of possible sequences encoded in the antigen-binding region and thus the repertoire of antigens that can be bound. Further variability is generated in antibody segments by two additional steps: (1) imprecise joining of gene segments, resulting in junctional diversity, and (2) DNA repair enzymes and terminal deoxynucleotidyl transferase activity removing and adding nucleotides randomly to the single-strand ends.

Whereas the antigen binding fragment (Fab) is responsible for the neutralizing and absorptive activities of antibodies, for immunoglobulins, the addition of different constant regions (M, D, G, E, and A) to the heavy chain, thus defining their isotype , imbues different functional activity on the molecule. These include different efficiencies in activating complement, binding to Fc receptors, and ability to cross the placenta. Immunoglobulin (Ig) D and IgM are translated from the same pre-mRNA transcript and are coexpressed on the surface of naïve, mature B cells. These heavy chains undergo instructional class-switching after first engagement with antigen, under the guidance of T cells. Importantly, transmembrane (B-cell receptor) and secreted (antibody) forms of these immunoglobulins are generated from the same mRNA transcript by differential splicing of mRNA to replace exons encoding a membrane anchor with exons encoding secretion sequences. These concepts are more thoroughly described in Chapter 2 . The secreted forms of antibodies have been extensively exploited in therapeutic settings, particularly once the development of monoclonal antibody hybridoma technology (where an immortalized B cell secretes large quantities of a single antibody) allowed the production of large quantities of homogeneous, highly defined antibody product. Some of the uses of monoclonal antibodies in cancer therapy are described in Table 7.1 .

Understanding the proteomic and genetic makeup of antibodies has allowed the further development of this resource beyond the initial hybridoma approaches to those that include isolation and expression of antibodies from individual B-cell clones and approaches that limit the inherent immunogenicity of murine proteins injected into humans. Note that exploration of synthetic TCRs as potential therapeutics, ^, targeting MHC–peptide complexes presented at the surface of tumor cells, is an ongoing and expanding field of research.

Signaling from T-cell receptor

For naïve T cells to proliferate and differentiate after engagement of the TCR by MHC–peptide complexes presented by dendritic cells (DCs), or for effector T cells to perform their functions upon reencountering their cognate antigen, signals must by propagated within the T cell, generally via the induction of enzymatic activity. Many of the common principles of receptor signaling were originally determined in the study of T cells. Knowledge of the mechanistic basis of TCR signaling has been critically important for understanding how checkpoint molecules such as Cytotoxic T lymphocyte Antigen -4 (CTLA-4) and Programmed Death 1 (PD1) work, and how the construction of more effective chimeric antigen receptor T cells (CAR-T) can be achieved.

Antigen-binding αβ T-cell receptor chains have no signaling capacity on their own. Rather, they associate with other molecules at the cell surface, CD3γ, CD3δ, CD3ε, and a ζ chain, which together form the CD3 complex (see Fig. 7.3 ). ^, The CD3 molecules are composed of immunoglobulin-like structures that have extracellular domains, and the ζ chain is primarily composed of a longer intracellular domain with only a short extracellular addition to the transmembrane domain. Critical to the ability to propagate signals, the intracellular domains of the CD3 proteins and the ζ protein contain immunoreceptor tyrosine-based activation motifs (ITAMs). ^, These ITAMs become phosphorylated by protein tyrosine kinases (PTKs) when the receptor complex engages its ligand. PTKs exist in two forms: as either intrinsic components of receptors (receptor tyrosine kinases [RTKs], such as the Fms-like tyrosine kinase 3 ligand (FLT3L) receptor) or as non-RTKs. An example of non-RTKs would be Janus Kinases (JAK) associated with cytokine receptors or Lymphocyte-specific protein tyrosine kinase (Lck) associated with the TCR. Non-RTKs are either constitutively associated with their receptors or are recruited after ligand binding. RTKs often multimerize to activate or are kept in inactive states by posttranslational modifications, as is the case with Lck.

B-cell receptor signaling

The BCR serves both as a signaling receptor, inducing the propagation of events that lead to functional changes within the B cell, and as an antigen-binding receptor for the purposes of antigen processing and presentation. Though in some instances, B cells can respond to antigen directly (T-independent antigens), these antigens tend to be associated with pathogenic infections and their allied adjuvant effects. Most B-cell responses require support of T cells, and the antigenic targets of these responses are referred to as T cell-dependent. Many aspects of BCR signaling are analogous to TCR signaling, because the antigen-binding domains of the BCR are associated with ITAM-containing components (Igα and Igβ) that transmute the signal. In place of Lck, B cells use the protein tyrosine kinases Fyn, B lymphoycte kinase (Blk) and Lyn to phosphorylate ITAMs after BCR multimerization. Spleen tyrosine kinase (Syk) serves as the ZAP-70 equivalent in B cells and it contains two SH2 domains that allow recruitment to the phosphorylated BCR. In each case, the primary proliferative signal from the BCR is communicated via PI-3 kinase-mediated activation of RAS/MAPK (mitogen activated protein kinase) pathway, inducing the activation of the transcription factors AP-1 and NFAT. The coreceptor functions of CD4 and CD8, and to a certain extent CD28 costimulation, are replaced in B cells by the CD19–CD21–CD81 complex. CD21 binds complement CD3dg–decorated antigen and the ensuing activation results in the activation of Src family tyrosine kinase. This promotes further Syk activation and the recruitment of the scaffolding protein SLP-65 (a LAT-SLP76 equivalent) to the BCR, and phosphorylation of CD19 permits the recruitment of phosphatidylinositol 3-kinase (PI3K). As a consequence of these activation events, the B cell can initiate remodeling events very similar to that seen in T cells, with phosphatidylinositol (3,4,5)-trisphosphase (PIP ₃ )/3-phosphoinositide-dependent kinase 1 (PDK1) leading to the activation of AKT, Bruton’s tyrosine kinase (BtK) leading to the activation of phospholipase C-gamma (PLC-γ) to make diacylglyceride (DAG) and inositol trisphosphate (IP3), and Vav activating Wiskott-Aldrich Syndrom Protein (WASP) and actin polymerization that precedes synapse formation that is necessary for antigen uptake and subsequent engagement of T helper cells. Targeting BtK is a therapeutic option for some B-cell malignancies.

CD28-signal 2

Antigen receptor binding (Signal 1) is insufficient to drive the full activation of naïve T and B cells. A second, conditioning, signal is needed to promote and sustain the activation and cycling of lymphocytes. In the case of T cells, in addition to TCR recognition of Ag/MHC complexes expressed on an APCs, such as a virus-infected dendritic cell, costimulatory signaling occurs via interaction between the costimulatory molecule CD28 and B7.1 or B7.2 (CD80/CD86), ^, if the APC expresses them. This leads to induction of both the high-affinity IL-2 receptor (IL-2Rα) and IL-2, which provides sufficient signals for proliferation, and the development of effector (cytotoxic) functions such as the generation of cytolytic granules. Recognition of the Ag–MHC complex is sufficient to drive the T cell from G0 into the G1 phase of the cell cycle but not through S phase (DNA replication). As such, the production of IL-2 can almost be considered a go–no go signal for T cells. Because Lck can also phosphorylate CD28 (if it is in the SMAC), ^, it can lead to the recruitment of growth factor receptor-bound protein 2 (Grb2), ultimately leading to the generation of more PIP ₃ . This has the effect of supporting the signaling modules described previously: PLCγ and downstream transcription factors, AKT and Vav, and the stabilization of IL-2 mRNA. CD28 stimulation is considered as Signal 2 in T-cell activation.

In the absence of Signal 2, T cells enter a state of unresponsiveness termed anergy . Anergy is not passive but is sustained by the expression of ubiquitin ligases such as gene related to anergy in lymphocytes (GRAIL) and c-Casitas B-lineaage (c-CBL) that actively degrade components of the TCR signaling process, limiting T-cell activation. ^, As might be anticipated, high doses of IL-2 can overcome the induction of anergy, likely by binding to the low-affinity IL-2βγ chain receptor. Anergy is induced in T cells when APCs are insufficiently activated (because of limited inflammation) to upregulate CD80 and/or CD86 but do present MHC–peptide complexes. This can occur in situations of peripheral tolerance (when new antigens arise as a function of developmental stages such as puberty) or in the case of slow-growing tumors. Importantly, the expression of CTLA-4, which serves as a competitor to CD28 on T cells for binding with CD80/CD86, ^, mimics the effects of encountering antigen without strong costimulation. Approaches that impede CTLA-4 have had some beneficial effects in several cancer entities. Other costimulatory molecules include IgSF members such as inducible costimulator (ICOS) and members of the tumor necrosis factor receptor superfamily (TNFRSF), such as CD27, OX40, and 41BB. Stimulation of TNF superfamily molecules promotes the expression and activity of c-Jun N-terminal kinase (JNK) via their regulation of tumor necrosis factor receptor-associated factor (TRAF) molecules and thus NF-κB. TNFRSF stimulation is primarily associated with T-cell survival, although some aspects of metabolic activity and memory cell differentiation have been attributed to these costimulatory molecules. TNFRSF receptors are often expressed 2 to 3 days after initial activation of DCs, providing a sustaining signal to activated T cells.

For B cells, the source of costimulation differs between the two types of antigens. T cell–independent BCR signals require support from the CD91–CD21–CD81 complex, which engages complement-bound antigens. This results in SH2-mediated enhancement of BCR signaling and the engagement of scaffolding signaling complexes that promote and multiply initial BCR signals. Further T cell–independent costimulation is supported by sensing additional pathogen-associated molecular patterns (PAMPs) from invading pathogens. These provide a MyD88-dependent activation of the NF-κB pathway that supports B-cell activation, analogous to the role of NF-κB in T cells.

The BCR serves both as a signaling receptor, inducing the propagation of events that lead to functional changes within the B cell, and also as a mechanism for internalizing antigen for presentation on MHC class II molecules, both turning the B cell into a professional antigen-presenting cell (APC). This ability to process and present antigen on MHC class II molecules allows B cells to interact with antigen-specific CD4 ⁺ T cells (in this case, T follicular helper cells [Tfh] located in the lymph nodes), which in turn support B cells by providing cytokines and receptor ligands that support B-cell proliferation and differentiation into either antibody-secreting cells or memory B cells (T cell–dependent processes). Tfh signals include CD40L, which provides survival advantages via the noncanonical NF-kB pathway (mediated by NF-kB-inducing kinase [NIK]) and the induction of the survival factor BCL2, and IL-21, which signals via signal transducer and activator of transcription 3 (STAT3) to promote proliferation and differentiation into memory and plasma cells. B cell–activating factor (BAFF; also known as B lymphocyte stimulator, BLyS), a member of the TNF superfamily, provides additional survival signals for maturing B cells.

Exhaustion

T-cell responses to cancer will be limited by the lack of costimulation during antigen presentation, leading to anergy, as described previously. In addition to anergy, T-cell responses within the tumor microenvironment are often curtailed because of the effect of chronic antigen presentation. ^, In this context, the consistent presence of antigen prevents the programmed acquisition of memory T-cell characteristics and the loss of pluripotent stemness. Aligned with this is a reduced expression of cytokines, reduced killing capacity, and limited proliferation. As with anergy, this altered state is driven by changes in transcriptional activity (e.g., the ratios of T-box expressed in T cells (Tbet): Eomesodermin (Eomes), T cell factor 1 (TCF1): Thymocyte Selection Associated High Mobility Group Box (TOX), ^, and B-cell lymphoma 6 (Bcl6): B lymphocyte-induced maturation protein-1 (BLIMP-1) ^, ) and the expression of a wide array of checkpoint inhibitor molecules, including Programmed Death-1 (PD-1), T cell immunoreceptor with Ig and ITIM domains (TIGIT), and T cell immunoglobulin and mucin domain-containing protein 3 (TIM-3) ( Table 7.2 ), whose ligands are commonly expressed in the tumor microenvironment (TME). The need for such an extensive network of counterstimulatory molecules is unclear. Transcriptional changes in exhausted T cells are quite distinct from those found in anergic T cells. Mechanistically, many of these molecules work by recruiting phosphatases (e.g., SHP2 in the case of PD1) that disrupt signal transduction pathways, thus attenuating signals from the TCR. Exhaustion is accompanied by metabolic alterations and, with time, epigenetic repression of key effector cell activities. Extensive studies in experimental models and in clinical trials have demonstrated the efficacy of targeting these checkpoint molecules for cancer immunotherapy. Correlates of responsiveness in patients include the presence of T cells within the patient’s TME and tumor mutational burden (TMB), which reflects the array of putative tumor antigens available for T cells to target. ^, In some instances, high doses of IL-2 or IL-7 can revert exhausted phenotypes.

Evidence for a similar exhaustion phenotype in B cells is mostly derived from studies of chronic/latent pathogen infections. B-cell exhaustion is also characterized by the expression of ITIM-containing inhibitory receptors, such as Fc receptor-like 4 (FCRL4) and sialic acid–binding Ig-like lectin 6 (Siglec-6) and downregulation of proliferative activity and BCR signaling. The presence and function of exhausted B cells in the tumor microenvironment has not been well documented.

Senescence

As with exhaustion, cellular senescence is a state of limited responsiveness that arises because of chronic antigen engagement and with aging (see T-cell subsets in cancer immunity ). Senescent T cells are characterized as having reduced telomere lengths and increased DNA damage, perhaps reflective of the combination of extensive replication and the age of the host. The DNA damage response found in senescent T cells can be induced both by tumor cells themselves as well as regulatory T cells found within the tumor microenvironment. Further characteristics that demark senescent T cells from exhausted include the absence of the costimulatory molecules CD27 and CD28, upregulation of molecules associated with terminal differentiation killer cell lectin like Rreceptor G1 (KLRG1; CD57), and the extensive production of proinflammatory and antiinflammatory cytokines. Some checkpoint molecules associated with exhaustion can also be expressed (e.g., TIM3, TIGIT) by senescent T cells. Proliferation is compromised by lesions in the proteins that are normally activated by TCR signaling, limiting the accumulation of phosphorylated signal transduction complexes.