T Cell Receptor Pathway Mutations in Mature T Cell Lymphomas

Abstract

Mature T cell lymphomas are heterogenous neoplasms that are aggressive and resistant to treatment. Many of these cancers retain immunological properties of their cell-of-origin. They express cytokines, cytotoxic enzymes, and cell surface ligands normally induced by T cell receptor (TCR) signaling in untransformed T cells. Until recently, their molecular mechanisms were unclear. Recently, high-dimensional studies have transformed our understanding of their cellular and genetic characteristics. Somatic mutations in the TCR signaling pathway drive lymphomagenesis by disrupting auto-inhibitory domains, increasing affinity to ligands, and/or inducing TCR-independent signaling. Collectively, most of these mutations augment signaling pathways downstream of the TCR. Emerging data suggest these mutations not only drive proliferation but also determine lymphoma immunophenotypes. For example, RHOA mutations are sufficient to induce disease relevant CD4⁺ T follicular helper cell phenotypes. Herein, we describe how mutations in the TCR signaling pathway elucidate lymphoma pathophysiology but also provide insights into broader T cell biology.

Introduction

Mature T cell lymphomas (TCLs) are a heterogeneous group of aggressive and poorly understood neoplasms(1). Broadly, there are >30 types distinguished by cell of origin, clinical presentation, and molecular markers. TCLs can originate from lymph nodes or from extranodal tissue, such as the skin or the gastrointestinal tract(2). The majority originate from memory CD4⁺ T cells and have features of CD4⁺ T cell effector states(3, 4). For example, angioimmunoblastic T cell lymphomas (AITLs) have features of T follicular helper cells (T_fh)(5); anaplastic large cell lymphomas (ALCL) may have features of T helper 17 (T_H17) cells(6); adult T cell leukemia/lymphoma (ATL), regulatory T cells (T_reg)(7); and peripheral T cell lymphoma-not otherwise specified (PTCL-NOS), T_H1 or T_H2 cells(8). Extranodal TCLs, such as cutaneous T cell lymphomas, are thought to arise from tissue resident memory cells(9). Less commonly, lymphomas are derived from cytotoxic T cells, such as γ T cells and CD8⁺ T cells(10). For the sake of brevity, we will not review the clinical aspects required to diagnose and/or treat these entities in full detail. For more information, please see the review by Cortes and Palomero(11).

Poor survival outcomes in T cell lymphomas are partly linked to an incomplete understanding of their disease biology. Recently, high-dimensional -omics have provided foundational insights into their pathophysiology. While our understanding of the circuitry remains incomplete, most TCLs harbor recurrent mutations in the TCR signaling pathway. These likely contribute to disease pathophysiology by promoting proliferation and by altering the effector molecules expressed by the malignant T cell. These immunologically active molecules are clinically relevant as they contribute to disease phenotypes. For instance, cytotoxic T cell lymphomas produce cytotoxic enzymes which lead to ulcerated tumors(12). Herein we will describe the recurrent mutations in the T cell receptor signaling pathway and their effects on protein structure, signaling, and immunophenotypes.

Proximal TCR Signaling

The TCR complex contains two TCR chains, six cluster of differentiation 3 (CD3) chains, and either a CD4 or CD8 co-receptor. There are four TCR genes in humans (α, β, γ, and δ) that form heterodimers. The CD3 complex is composed of γ, δ, ε, and ζ subunits containing cytosolic immunoreceptor tyrosine-based activation motifs (ITAMs) that mediate intracellular signals. Non-covalent hydrophobic interactions associate the TCR heterodimer with the CD3 complex(13).

Antigens are presented by nucleated or antigen-presenting cells on major histocompatibility complex (MHC) class I or class II, respectively. TCR ligands are MHC molecules containing a peptide in the binding groove(14). Engagement of the TCR-MHC complex with sufficient affinity activates a series of protein tyrosine kinases (PTKs). LCK and FYN are Src-family PTKs that contain an Src homology 4 (SH4) lipid attachment domain, SH3, SH2, and tyrosine kinase (TK) domain(15–17). Upon TCR engagement, LCK is recruited to the immune synapse and subsequently phosphorylates the TCR CD3-associated ITAMs to recruit another PTK, ZAP-70, and to initiate signal transduction(16). FYN and ITK are subject to gain-of-function point mutations and translocations in TCLs. These proximal PTKs activate scaffolding proteins (e.g., LAT, GADS, and SLP-76) that recruit and activate downstream enzymes such as PLCγ1, VAV1, and RHOA. Signals converge at hubs such as the CARD11/BCL10/MALT1 (CBM) complex and activate downstream nuclear factor of activated T-cells (NFAT), activator protein-1 (AP-1), nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB), and mammalian target of rapamycin (mTOR) signaling pathways(18–20). These pathways mediate multiple aspects of TCR-dependent biology, including both T cell proliferation and production of pro-proliferative cytokines such as interleukin-2 (IL-2)(21). Broadly, most TCR mutations in lymphomas activate one or more of the signaling pathways downstream of the TCR, e.g., the NFAT, AP-1, and NF-κB pathways (Figure 1).

Figure 1. T cell receptor signaling pathway members and frequency of SNVs and CNVs in AITL, ATL, CTCL, and PTCL-NOS.

T cell signaling pathway members discussed previously are shown. Proximal PTKs activate scaffolding proteins (e.g., LAT, GADS, and SLP-76) that recruit and activate downstream enzymes such as PLCγ1, VAV1, and RHOA. Signals converge at hubs such as the CARD11/BCL10/MALT1 (CBM) complex and activate downstream nuclear factor of activated T-cells (NFAT), activator protein-1 (AP-1), nuclear factor kappa-light-chain enhancer of activated B cells (NF-κB), and mammalian target of rapamycin (mTOR) signaling pathways. A red border signifies genes with oncogenic mutations described above. A blue border denotes a tumor suppressor role in TCLs. The SNV and CNV frequencies in a cohort of AITL, ATL, CTCL, and PTCL-NOS (including T_fh-PTCL) samples as previously described are shown(28, 29, 40, 60, 62, 63, 95, 129). Red: AITL; Yellow: ATL; Blue: CTCL; Purple: PTCL-NOS. The SNV frequency is displayed for AITL, ATL, CTCL, and PTCL-NOS in the first row in darker color. The CNV frequency is displayed for ATL, CTCL, and PTCL-NOS in the second row in lighter color.

FYN contributes to proximal TCR signaling by phosphorylating ZAP70 and other substrates(22, 23). It is kept in an inactive basal state by C-terminal Src kinase (CSK), which phosphorylates FYN at the C-terminus p.Y531, providing a phosphotyrosine to bind to the FYN SH2 domain. The SH3 domain binds the linker between the SH2 and kinase domain; altogether, these interactions restrict the movement of the kinase domain, inhibiting catalytic activity(24–26). Sequential biochemical interactions disentangle the inhibitory domains from the kinase domain during TCR signaling(27). For example, a conserved tryptophan between the linker and kinase domain interacts with a hydrophobic region in the αC helix and the residue rotates out of the helix during activation(27). FYN is mutated in 3–4% of AITL, ATL, and PTCL-NOS (Figure 1)(24, 28, 29). Mutations cluster in the SH3, SH2, and the C-terminus domains are predicted to prevent the inhibitory intramolecular interactions between 1) the C-terminus and the SH2 domain or 2) between the SH3 domain and linker region(Figure 2A)(24, 28). For example, SH2 domain mutations (p.L174R, p.R176C) prevent its binding to the phosphorylated p.Y531, while the C-terminal truncations or mutations (p.Y531H) eliminate the phosphorylation site critical for the autoinhibitory SH2-C-terminus interaction (Figure 2B)(24).

Figure 2. SNVs in TCR signaling pathway members disrupt key regulatory domains.

The mutation locations within protein domains are shown in the lollipop diagrams (created with trackViewer(130)). The pie graph above a mutation position contains the percentage of the mutations within a gene that lie at the location for each TCL(26, 47, 69, 75, 131). They are ordered, from bottom to top, as AITL (red), ATL (yellow), CTCL (blue), and PTCL-NOS (purple). The autoinhibition mechanisms of TCR pathway members are shown in the structural diagrams. Point mutations affecting key domains are marked with a lightning bolt. Truncating mutations are marked with a stop figure. The left figures labeled “inhibited” show the interactions at basal state. The right figure labeled “activated” show the active conformation and the effects of mutations. A. Point mutations of FYN frequently occur in the SH3, SH2, and kinase domains. The most commonly mutated sites are p.R96 and p.R176. B. FYN is autoinhibited by the SH2 domain interacting with the C-terminus Y527 and SH3 domain interacting with the SH2-kinase linker domain. The Trp264 residue interacts with the αC helix of the kinase domain. During activation, the kinase domain is free to bind substrate. C-terminus mutations/truncations or mutations in the SH2 or SH3 domains disrupt the inhibitory interaction. C. Point mutations in PLCG1 frequently occur in the PH, catalytic, and C2 domains. The most commonly mutated sites are p.R48, p.S345, p.E1163, and p.D1165. D. The PLCG1 p.Y783 site is phosphorylated during activation and frees the catalytic core by binding to the C-SH2 domain. Mutations in the catalytic core or in the PH domain disrupt the autoinhibitory interface, allowing the catalytic core to access substrate. E. Point mutations in VAV1 frequently occur in the acidic linker region, PH, ZF, and C-SH3 domains. The most commonly mutated site is p.E556. F. VAV1 autoinhibition is mediated by Ac, PH, and CH domains that block the DH domain active site. Mutations in the Ac or DH domain disrupt the autoinhibition. Truncating or point mutations in the C-terminal SH3 domain are also frequently seen in TCLs. G. Point mutations in RHOA frequently occur in the GTP binding domains. The most commonly mutated site is p.G17. H. Point mutations in PRKCB frequently occur in the protein kinase domains. The most commonly mutated site is p.D427. I. PRKCB features a C1b domain that sequesters the essential p.F629 residue from the active site during autoinhibition. Mutations in the protein kinase N-lobe allow activation independent of upstream kinases. J. Point mutations in CARD11 frequently occur in the coiled coil and inhibitory domains. The most commonly mutated sites are p.D401 and p.E626. K. CARD11 forms an autoinhibited structure featuring multiple interactions with the inhibitory domain (ID). Phosphorylation of the domain activates CARD11. Mutations affecting the ID domain or linker region enables autonomous activation of CARD11.

Interleukin-2 tyrosine kinase (ITK) belongs to the Tec family of protein kinases. It is activated and recruited to the membrane by two mechanisms(30, 31). ZAP70 phosphorylates the adaptors LAT and SLP-76, which contain binding sites for the SH2 and SH3 domains of ITK(32). Simultaneously, co-stimulation through CD28 activates PI3K and produces PIP₃, the attachment site of the ITK plekstrin homology (PH) domain. Activated ITK subsequently phosphorylates phospholipase C gamma (PLCγ1)(33, 34). In PTCL-NOS, there are recurrent ITK-SYK fusions linking the PH and TH domains of ITK with the kinase domain of the spleen tyrosine kinase (SYK)(35). The PH domain of ITK enables the fusion transcript to constitutively localize to lipid rafts near the sites of TCR signaling. This appears to be sufficient to enable phosphorylation of proximal signaling proteins in a TCR independent manner (36).

PLCG1

Following activation by proximal PTKs, PLCγ1 catalyzes the conversion of phosphatidylinositol-4,5-bisphosphate (PIP₂) to inositol-1,4,5-triphosphate (IP₃) and diacylglycerol (DAG). PLCγ1 consists of an N-terminal PH region, an EF region, a catalytic X-Y domain with a γ1-specific array of SH2 and SH3 modules, and a C2 domain(37). Point mutations in PLCG1 are frequent in T cell neoplasms: 11% of AITL, 36% of ATL, 10% of CTCL, and 9% of PTCL-NOS (Figure 1)(28, 29, 38). They occur in the loop regions of the TIM-barrel surfaces that form the active site opening and in the C2, cSH2, and PH domains (Figure 2C)(39). These mutations increase production of IP₃ and uniformly activate NFAT and AP-1, but variably activate NF-κB(38, 40, 41).

Normally, PLCγ1 is maintained in an inactive state by auto-inhibitory interactions between the catalytic X-Y domain and inhibitory C2, PH, and two SH2 domains, preventing the DH domain from binding lipid substrates (Figure 2D)(39, 42). Phosphorylation of p.Y783 disrupts the autoinhibitory interface and enables hydrolysis at the active site. p.S345F in the TIM barrel and p.S520F in the PH domain disrupt the autoinhibitory domain interactions and thus no longer require phosphorylation of p.Y783 for PLCγ1 kinase activity(43).

PLCG1 mutations have also been proposed to increase phosphodiesterase activity by increasing plasma membrane affinity and interaction with the PIP₂(41). p.R48W, p.S345F, p.E1163K, p.D1165H, and p.VYEEDM1161V act through this mechanism(38, 44). Furthermore, the PLCG1 indel, p.VYEEDM1161V, reported in SS(45), occurs in the hotspot C2 domain of PLCG1, a calcium-dependent, membrane targeting module. p.VYEEDM1161V resulted in decreased expression of PLCγ1, suggesting that the indel affects protein stability and may lead to faster degradation of PLCγ1. Nevertheless, it increased phosphorylation of Y783 and is one of the most potent activators of NFAT compared to other PLCG1 mutations(38).

VAV1

VAV1, a guanine nucleotide exchange factor (GEF), activates Rho family GTPases RAC1, RHOA, and CDC42(46). It also has catalysis-independent mechanisms as an adaptor protein to activate the PLCγ1-dependent pathway, stimulating NFAT. VAV1 contains eight domains: N-terminal calponin homology (CH) and acidic (Ac) domains, Dbl homology (DH) and pleckstrin homology (PH) domains that make up a catalytic core, zinc finger (ZF), and C-terminal SH2 and SH3 domains. The active site (DH) is inhibited through multiple interactions with the Ac, PH, and CH domains that block access to substrate and inhibit GEF activity (Figure 2E)(47). The SH3 domain interacts with the PH and catalytic domains to stabilize these interactions and occlude the catalytic domain from substrates(48). The highly conserved p.Y174 position in the Ac region acts as a molecular lock by facilitating the binding of the inhibitory helix to the DH active site(47). Phosphorylation of p.Y174 by LCK and ZAP70 displaces the inhibitory helix from the DH domain and frees the active site to bind substrate (Figure 2F)(47).

VAV1 alterations in TCLs encompass point mutations, focal intragenic deletions that affect splicing, and gene fusions that delete the autoinhibitory C-terminal SH3 domain. Point mutations in VAV1 are frequently found in 5% of AITL, 18% of ATL, 1% of CTCL, and 6% of PTCL-NOS (Figure 1)(28, 29). Hotspots occur in the acidic, PH, zinc finger, and C-terminal SH3 domains that regulate VAV1. These mutations, such as p.Y174C in ATL, abolish the autoinhibitory interactions between the DH and Ac domains; the mechanism of the zinc finger domain mutations is uncertain(28). VAV1 mutations activate PLCγ1 and subsequently NFAT. It can also activate RAC1, with downstream effects on cytoskeleton remodeling and increased cJun N-terminal kinase (JNK) activity, which in turn activates the AP-1 signaling pathway(49).

Structural variants of VAV1 occur in PTCL-NOS, AITL and ALCL. The 778–786 deletion in PTCL is caused by a splice site mutation within the linker region between the SH2 and C-terminal SH3 domains(50). VAV1 rearrangements, such as VAV1-MYOF1 and others, eliminate the C-terminal SH3 domain of VAV1 and enable it to energetically favor the open, disinhibited configuration(50–52).

Analogous to the SH3 domain point mutations, the VAV1-MYO1F fusion increases basal activation of VAV1-dependent signaling cascades, including MAPK (ERK1/2), JNK, and NFAT, which are further augmented by TCR stimulation. These cells have increased expression of MAF following CD3 and CD28 stimulation, preferential IL-4 secretion with stimulation by PMA/ionomycin, and enrichment of T_H2 transcription signatures(53). These data suggest that a modification of TCR-associated signaling enzymes is sufficient to induce T_H2 differentiation. Mechanistically, this may promote lymphomagenesis in part by creating a pro-tumor T_H2 microenvironment and polarizing M2 tissue-resident macrophages(53). Notably, GATA3⁺ PTCL-NOS are the most aggressive of PTCL subtypes, suggesting the clinical importance of these genotype-phenotype interactions.

Structural rearrangements in VAV1-associated enzymes are common in ALCLs. The nucleophosmin (NPM)-anaplastic lymphoma kinase (ALK) fusion combines the oligomerization domain of NPM with the C-terminal TK of ALK. It generates a constitutively active tyrosine kinase that defines a subset of ALK⁺ ALCLs. The fusion protein is essential for ALCL growth and survival by activating the STAT3, MEK/ERK, and PI3K/AKT pathways(54–58). The fusion complexes with and phosphorylates VAV1, leading to upregulation of downstream small G-proteins such as CDC42 and RAC1(59). RAC1 and CDC42 regulate actin polymerization with ARP2/3, contributing to the shape and migration phenotype in ALCL similar to that of activated T cells(54).

RHOA

RHOA is a small GTPase activated upon TCR stimulation by specific GEFs, and it regulates the actin cytoskeleton, cell development, and proliferation. AITL (68%), ATL (8%), CTCL (5%), and PTCL-NOS (22%) have hotspot RHOA mutations (Figure 1). Notably, their oncogenic role varies depending on the cell of origin(60, 61).

The GTP binding domains of RHOA are recurrently mutated in TCL (Figure 2G). The p.G17V and p.A161D in AITL and p.N117I/K in CTCL have a dominant negative effect by sequestering upstream RhoGEFs and decreasing levels of RHO-GTP. In contrast, the p.C16R and p.A161P in ATL are gain-of-function and have increased GDP/GTP cycling rate and increased transcriptional activation(24, 60–62). How RHOA mutations with distinct biochemical effects all support traditional cancer phenotypes, such as cell proliferation, during lymphomagenesis remains unclear.

Nonetheless, specific RHOA mutations have an impact on cell phenotypes. ATL cells carrying a WT or activating RHOA mutation (p.C16R/G, or p.A161P) have a Treg or effector T cell phenotype, while those carrying an inactivating RHOA mutation (p.G17V) have a memory T cell phenotype(60). RHOA p.G17V alteration accounts for 95% of RHOA mutations in AITL and 88% of RHOA mutations in PTCL-NOS (including T_fh-PTCL)(24, 29, 63, 64). Expression of the mutant RHOA isoform in premalignant cells is sufficient to induce expression of canonical T_fh markers PD-1, ICOS, CXCL13, BCL6, and CD10(65). The T_fh transcription factor BCL-6 and T-B interaction through SAP are required for AITL proliferation and lymphomagenesis(66). A mouse model of AITL generated with a p.G17V mutation led to proliferation of T_fh-like cells in lymph nodes with increased germinal center activity and plasma cell infiltration(61, 67).

Distal TCR Signaling

Protein Kinase C

Protein kinase C theta (PKC-θ, PRKCQ) and protein kinase C beta (PKC-β, PRKCB) are phosphorylated by PLCγ1 and, in turn, phosphorylate CARD11, a component of the CBM complex(68). The N-terminal pseudosubstrate region of PKC inhibits the C-terminal kinase domain via the Asn-Phe-Asp (NFD) motif. Receptor stimulation recruits PKC to the cell membrane via two interactions: the C2 domain binding to Ca²⁺ and phospholipids and DAG binding to the C1 domains(68). Normally, the C1b domain sequesters p.F629 of the NFD domain and prevents its projection into the ATP binding site. DAG engagement of the C1 domain frees p.F629 to participate in hydrolysis (Figure 2I)(69).

PKC-θ and PKC-β are mutated in CTCL and ATL (Figure 1)(28, 70). PRKCQ is amplified in 30% of CTCL, leading to increased STAT3 and NFAT activation(70, 71). PRKCB is mutated in 33% of ATL and 1% of CTCL, with more than 90% of mutations clustering in the enzymatic domain (Figure 2H)(72). D427 and D630 mutations obviates the need for activation by upstream kinases(72). The p.D427 residue is near p.Y422 and p.Y430 that stabilize the C1b-NFD interaction and the p.D630 residue is within the NFD motif; destabilization of either of these regions causes activation(72). PRKCB p.D427N thus increases IκB kinase (IKK) phosphorylation and subsequent downstream NF-κB transcription(28).

The CBM Complex

Caspase recruitment domain-containing protein 1 (CARD11/CARMA1) is a scaffolding protein containing an N-terminal caspase activation and recruitment (CARD) domain, coiled-coil domain, linker domain, PDZ domain, and a membrane associated guanylate kinase (MAGUK)(73). CARD11 is auto-inhibited by an interface involving the linker and coiled-coil domains(74). Activated PKC phosphorylates the inhibitory domains (IDs) located near the linker region and disrupt the inhibitory interface that sequesters the CARD domain (Figure 2K)(75, 76). The open CARD11 scaffold can recruit its binding partners BCL10 and MALT1 to form a stable oligomeric complex with additional enzymes and scaffolding proteins. For example, it attracts and polyubiquitinates TRAF6 at the SH3/PDZ domain(76, 77).

CARD11 point mutations in TCLs occur in the linker, coiled-coil, and inhibitory domains (Figure 2J). They are present in 24% of ATL and 2–5% of AITL, CTCL, and PTCL-NOS (Figure 1)(28, 29, 40, 70, 78). Copy number gains often accompany CARD11 mutations; 12% of ATL have gene amplifications and recurrent small intragenic deletions in the inhibitory domains(28). Mutations at the coiled-coil and linker regions typically disrupt the autoinhibitory interaction increase response and increase NF-κB activity following TCR signaling(28, 40, 78). For example, a mouse model of the ATL p.E626K mutation was sufficient to activate NF-κB biochemically, leading to effector/memory and regulatory T cells activation and local tissue destruction(79).

RLTPR

RLTPR is a scaffolding protein that bridges CD28 to the CARD11 adaptor (Figure 1)(63). It has no enzymatic domains. Instead, it harbors an essential PH domain, leucine-rich repeat (LRR), and proline-rich region (PRR); the LRR is necessary for colocalization with CARD11(63). The PRR mediates signals from CD28 through attachments involving GRB2/GRAP2(80). Functional RLTPR is essential for differentiation into T_H1, T_H17, and T_reg cells(80, 81). RLTPR mutations (found in 3% of CTCL and 8% of ATL) cluster at p.Q575, with is located on the surface-exposed, convex side of the LRR region(19, 49). p.Q575E dramatically increases association with CARD11(62). However, in the absence of TCR activation, it does not appear to functionally alter the cell. For example, p.Q575E augments gene transcription (e.g., NF-κB activity) and IL-2 production only in cells stimulated with chemical TCR mimics but not in unstimulated controls(49, 64). These data suggest CTCLs must undergo repeated chronic or tonic TCR stimulation to provide selection pressure for its recurrence rate(49, 64).

CSNK1A1

CSNK1A1 encodes casein kinase 1a, a serine/threonine kinase that consists of an N-terminal catalytic domain coupled to a C-terminal variable region(82). It has dual function in T cells: it first associates with the CBM complex following TCR engagement to recruit IKK to phosphorylate IκB and activate NF-κB; then, it phosphorylates and inactivates CARD11 to attenuate signaling (83). CSNK1A1 has recurrent mutations in CTCL and ATL at p.S27 (p.S27F/C)(62). These alterations occur at the tip of the phosphate binding, glycine-rich P-loop in the kinase domain of CK1a(62). The P-loop is a structure shared by protein kinases that normally blocks binding of the peptide substrate to the active site residues and is relieved by phosphorylation(84). In lung cancer, epidermal growth factor receptor (EGFR) mutations in the P-loop domain, which share a similar function, result in enhanced kinase activity(85). These mutations cause increased expression of IL-2 in response to TCR stimulation with CD86 co-stimulation in Jurkat cells, suggesting they potentiate its pro-NF-κB signaling(62).

Costimulatory Molecules

CD28

CD28 belongs to a family of surface receptors, including cytotoxic T-lymphocyte-associated protein 4 (CTLA4) and inducible costimulator (ICOS), that are covalent homodimers with immunoglobulin domains attached to transmembrane and cytoplasmic tyrosine signaling motifs(86). It is a co-stimulatory receptor that binds to the ligands CD80 (B7.1) or CD86 (B7.2) for full proliferation and cytokine production following TCR engagement(87). CD28 and ICOS contain activating tyrosine domains, while CTLA4 contain inhibitory tyrosine domains; the balance between these signals governs T cell phenotype(88). CTLA4 interacts with two CD86 molecules and has 50–100 times higher binding affinity for CD86 than CD28, which only binds one CD86 molecule(89).

CD28 point mutations occur in 13% of AITL and 2–4% of ATL and CTCL (Figure 1). A subset of the CD28 mutations combine properties of the extracellular domain of CTLA-4 with the intracellular activating domains of CD28. First, there are CTLA4-CD28 fusions which link the CTLA4 extracellular domain to the CD28 intracellular domain(28, 90). Second, there are point mutations that make CD28 more avid for their ligands and thus their extracellular domain more CTLA-4-like. For example, there are three highly conserved residues between CD28 and CTLA4 in analogous positions of the C beta strand(86). p.F51V in CTCL and ATL modify the Glu-Phe-Arg residues on the C beta strand of the IgV domain in CD28 to mimic the Glu-Val-Arg residues on the C beta strand of IgV domain in CTLA-4(28, 70, 86). This substitution increases mutant CD28’s avidity for CD86 but not for CD80(28, 70).

Intracellular mutations, e.g., p.T195P/I in AITL, ATL, and PTCL-NOS, are located between the SH2 binding motif and the SH3 binding motif near the C-terminus. They increase the affinity of CD28 for the adaptor proteins GRB2 and GRB2-related adaptor protein 2 (GADS/GRAP2) compared to wild-type CD28(28, 91). This leads to increased ligand-dependent NF-κB activity and cytokine expression in Jurkat cells(91).

Inhibitors of TCR Signaling

PD1/PD-L1

Programmed cell death protein 1 (PD1) is an inhibitory receptor on activated T cells that engages the ligands PD-L1 and/or PD-L2. It inhibits TCR and CD28 activation biochemically and phenotypically promotes T cell dysfunction associated with chronic TCR activation, colloquially called T cell exhaustion(92). Unlike costimulatory proteins, PD1 has intramembrane domain with immunoreceptor tyrosine-based inhibitory motif (ITIM) and immunoreceptor tyrosine-based switch motif (ITSM) domains that recruit tyrosine phosphatases, which dephosphorylate enzymes critical for TCR signaling, i.e., ZAP70, LCK, and PI3K(93).

Deletions and pharmacologic inhibition have demonstrated PD1 acts as a haploinsufficient tumor suppressor in TCLs(94). PDCD1 damaging mutations are present in 23% of mature T cell neoplasms (Figure 1)(94). PD1 inactivating mutations contribute to the development of aggressive and serially transplantable lymphomas in mouse models(94). In patients, PD1 loss is associated with increased clinical stage of disease and shorter survival in CTCL(95). Mechanistically, CTCLs with PDCD1 gene locus deletions have decreased exhaustion and increased proliferation compared to PD1-wild type samples(95). Highlighting its role as a tumor suppressor, PD1 blockade with a blocking antibody (nivolumab) in acute, smoldering, and chronic ATL led to rapid disease progression(96).

TNFAIP3

Tumor necrosis factor-α-induced protein 3 (TNFAIP3/A20), is a negative regulator of the NF-κB signaling pathway that contains an N-terminal deubiquitinating enzyme targeting K63 polyubiquitin chains and a C-terminus zinc finger domain that ubiquitinylates at p.K48(97). p.K63 polyubiquitinated TRAF6 and RIP serve as scaffolds for ubiquitin-binding domain proteins and recruit transforming growth factor beta-activated kinase (TAK1) and IκB kinase (IκK) to activate NF-κB; TNFAIP3 removes p.K63 polyubiquitination while ubiquitinating at p.K48, which decreases NF-κB activity(98). TNFAIP3 is a transcriptional target of NF-κB, and is thought to act in a negative feedback mechanism to terminate NF-κB signaling(99). TNFAIP3 is deleted in 25% of CTCL (Figure 1); deletion of one copy abrogates the need for CD28 co-stimulation and causes hyperproliferation following TCR stimulation(70, 100, 101).

Transcription Factors Downstream of TCR Signaling

NF-κB

Gain-of-function mutations in the TCR pathway (CARD11(78), CD28(91), PLCG1(40), and RLTPR(62)) activate NF-κB. The NF-κB subunit family includes p50 and its precursor p105 (NFKB1), p52 and its precursor p100 (NFKB2), RelA (p65), RelB, and c-Rel(102). Each subunit has a Rel homology region, containing an N-terminus domain, a dimerization domain, and a C-terminus nuclear localization signal(103). The transcription activation domain is present in RelA, RelB, and c-Rel; NF-κB dimers containing one of these three subunits is required for transcription activation(104, 105). IκB family members contain a series of six ankyrin repeats that mask the nuclear localization signal of the NF-κB heterodimers, sequestering them in the cytoplasm. IκB phosphorylation by the IκK complex during T cell activation targets IκB for degradation, allowing NF-κB heterodimers to interact with their target DNA sequences(103, 106, 107). Notably, p105 and p100 also contain C-terminal ankyrin repeats that act as IκB domains, which sequester the full-length protein in the cytoplasm. With IκK activation, this part of the protein is ubiquitinated and degraded by the proteasome, enabling the N-terminus p50 or p52 to translocate to the nucleus(108, 109).

NF-κB transcription factors can themselves be mutated. Structural alterations of NF-κB subunits increase proliferation and survival in CTCL and ATL in a cell-intrinsic manner(72, 95). C-terminal truncations or splice site mutations of NFKB2 are found in 12.5% of CTCL (especially in late-stage leukemic disease)(62, 70). They simulate constitutive degradation of the C-terminal IκB like domains and free NFKB2 from cytoplasmic sequestration, causing constitutive nuclear localization and activation of the non-canonical NF-κB pathway(70, 110).

ZEB1

Zinc finger E-box binding homeobox 1 (ZEB1) is a transcriptional repressor. It is an oncogene involved with epithelial-mesenchymal transition (EMT), metastasis, and drug resistance in many epithelial cancers(111, 112). However, it appears to be a tumor suppressor in TCLs(113–115). For example, ZEB1 is deleted or subjected to inactivating point mutations in 65% of CTCL(70). ZEB1 has many putative immunologically relevant mechanisms inferred from older studies performed on T cell lines. However, in mouse and human primary T cells, ZEB1 appears to be mostly necessary for Janus kinase 2 (JAK2) dependent T_H1/T_H17 fate determination and suppression of T_H2 differentiation(116–119). The mechanisms by which ZEB1 supports lymphomagenesis is not clear, but ZEB1 inactivating mutations may affect the immunophenotype of the lymphomas, i.e., the cytokines produced by the lymphoma cells(120).

IRF4

The c-Rel/NF-κB complex binds to the IRF4 promoter upon TCR stimulation(121). Interferon regulatory factor 4 (IRF4) is a transcription factor essential for metabolic reprogramming in T cell proliferation. It is also critical for the T_H1, T_H2, T_H9, T_H17, and T_fh lineages, making its role in lymphomagenesis is unclear(122–124). It consists of a DNA binding domain, a linker domain, and an interferon association domain(125). Point mutations and translocations in IRF4 in TCLs overexpress or increase activity of IRF4. In ATL, a mutation in IRF4 occurs at the highly conserved p.K59. p.K59R preserves the DNA binding function but prevents ubiquitination, leading to increased protein half-life and increased activity(125). Expression of p.K59R in murine bone marrow cells caused T cell proliferation(125).

BACH2

Broad complex-tramtrack-bric a brac and Cap’n’collar homology 2 (BACH2) is a transcription factor that limits the expression of TCR-driven genes by reducing the accessibility of AP-1(126). BACH2 was first described as a novel tumor suppressor in CTCL(127). It is mutated in 14% of CTCL samples via intragenic translocations that uncouple its coding sequences from its promoter or via transposon insertions in the BACH2 gene locus(95). This appears clinically relevant as the gene is inactivated in 25% of lymphomas that develop from chimeric antigen receptor T cells (CAR-Ts)(128). These invariably decreased BACH2 expression and were linked to higher rates of development into CAR-T cell lymphomas(127). It remains unclear if the prevalence of these mutation in CAR-T derived lymphomas were due to selection for BACH2 insertion or as a preference for insertion in the region(127).

Conclusions

Integrated genomic analyses of TCLs have revealed recurrent mutations in the TCR signaling pathways. Often, mutations share similar mechanisms, such as loss of inhibitory domains, disruption of intramolecular interactions, and increased catalytic activity. The phenotypic manifestations of T cell neoplasms are a direct consequence of the cell of origin, specific genetic derangements, and nearby cell signals. Certain mutations appear to be disease defining, e.g., RHOA p.G17V for AITL. These appear to be sufficient to affect the immunophenotype of the malignant T cell leading to clinically relevant inflammation. In summary, human T cell lymphomas offer a human genetic model system to study the regulation of TCR-associated molecules and their functional importance. Although much has been learned biochemically in experimental systems, how these mutations affect primary cells in their native microenvironments remains unclear. Spatial transcriptomics and single-cell studies of these lymphomas may reveal fundamental insights on immune cell interactions. Cell lines and mouse models that capture specific immunophenotypes may be generated to explore effector interactions that cause pathology. Lastly, further studies will be required combining understanding of tumor biology with biochemistry to elucidate mechanisms that can be targeted to benefit patients with these diseases.

1. J.C. was supported, in part, by an American Cancer Society Research Scholar Award, Leukemia and Lymphoma Society, Chicago Biomedical Consortium, National Comprehensive Cancer Network, National Institutes of Health (NIH), National Cancer Institute (NCI), National Institute of Allergy and Infectious Diseases Extramural Activities, the Skin Cancer Foundation, the Leukemia Research Foundation, the Doris Duke Charitable Foundation, and the Damon Runyon Foundation.

Abbreviations used:

TCR

T cell receptor

TCLs

T cell lymphomas

AITL

angioimmunoblastic T cell lymphoma

ALCL

anaplastic large cell lymphoma

ATL

adult T cell leukemia/lymphoma

PTCL-NOS

peripheral T cell lymphoma-not otherwise specified

T_H1

T helper 1

T_H2

T helper 2

T_H17

T helper 17

T_reg

regulatory T cell

CD3

cluster of differentiation 3

ITAM

immunoreceptor tyrosine-based activation motif

MHC

major histocompatibility complex

PTK

protein tyrosine kinase

SH

Src homology

TK

tyrosine kinase

CBM

CARD11/BCL10/MALT1

NFD

Asn-Phe-Asp

IKK

IκB kinase

CARD11/CARMA1

caspase recruitment domain-containing protein 1

NF-κB

nuclear factor kappa-light-chain enhancer of activated B cells

mTOR

mammalian target of rapamycin

CSK

C-terminal Src kinase

PLCγ1

phospholipase C gamma

SYK

spleen tyrosine kinase

PIP₂

phosphatidylinositol-4,5-bisphosphate

IP₃

inositol-1,4,5-triphosphate

DAG

diacylglycerol

AP-1

activator protein-1

GEF

guanine nucleotide exchange factor

CH

calponin homology

Ac

acidic

DH

Dbl homology

PH

plekstrin homology

ZF

zinc finger

JNK

c-Jun N-terminal kinase

NPM

nucleophosmin

ALK

anaplastic lymphoma kinase

PKC

protein kinase C

PKC-θ

protein kinase C theta

PKC-β

protein kinase C beta

CARD

caspase activation and recruitment

MAGUK

membrane associated guanylate kinase

ID

inhibitory domain

LRR

leucine rich repeat

PRR

proline-rich region

EGFR

epidermal growth factor receptor

CTLA4

cytotoxic T-lymphocyte-associated protein 4

ICOS

inducible costimulator

IL-2

interleukin-2

GRB2

growth factor receptor bound protein

GADS/GRAP2

GRB2-related adaptor protein 2

PD1

programmed cell death protein 1

ITIM

immunoreceptor tyrosine-based inhibitory motif

ITSM

immunoreceptor tyrosine-based switch motif

PTEN

phosphatase and tensin homolog deleted on chromosome 10

TNFAIP3

tumor necrosis factor-alpha-induced protein 3

TAK1

transforming growth factor beta-activated kinase

IκK

IκB kinase

ZEB1

zinc finger E-box binding homeobox 1

EMT

epithelial-mesenchymal transition

JAK2

Janus kinase 2

HDAC

histone deacetylase

IRF4

interferon regulatory factor 4

BACH2

Broad complex-tramtrack-bric a brac and Cap’n’collar homology 2

CAR-T

chimeric antigen receptor T cell