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CD3ζ ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides

Nature Immunology volume 24, pages 2121–2134 (2023)Cite this article

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A Publisher Correction to this article was published on 06 December 2023

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Abstract

The T cell antigen receptor (TCR) contains ten immunoreceptor tyrosine-based activation motif (ITAM) signaling sequences distributed within six CD3 subunits; however, the reason for such structural complexity and multiplicity is unclear. Here we evaluated the effect of inactivating the three CD3ζ chain ITAMs on TCR signaling and T cell effector responses using a conditional ‘switch’ mouse model. Unexpectedly, we found that T cells expressing TCRs containing inactivated (non-signaling) CD3ζ ITAMs (6F-CD3ζ) exhibited reduced ability to discriminate between low- and high-affinity ligands, resulting in enhanced signaling and cytokine responses to low-affinity ligands because of a previously undetected inhibitory function of CD3ζ ITAMs. Also, 6F-CD3ζ TCRs were refractory to antagonism, as predicted by a new in silico adaptive kinetic proofreading model that revises the role of ITAM multiplicity in TCR signaling. Finally, T cells expressing 6F-CD3ζ displayed enhanced cytolytic activity against solid tumors expressing low-affinity ligands, identifying a new counterintuitive approach to TCR-mediated cancer immunotherapy.

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Fig. 1: 6F(i)-CD3ζz T cells exhibit enhanced activation responses to some LCMV ligands.
Fig. 2: 6F-CD3ζ-expressing T cells have a lower threshold of activation to low-affinity antigens but are not overtly self-reactive.
Fig. 3: 6F-CD3ζ-expressing T cells display enhanced TCR signaling when stimulated with low-affinity peptides.
Fig. 4: Antigen-stimulated OTI-6F(i) CD8+ T cells exhibit reduced ligand discrimination.
Fig. 5: 6F-CD3ζ TCRs do not recruit or retain SHP1 and are associated with more pZAP-70 after pMHC engagement.
Fig. 6: 6F-CD3ζ-expressing T cells have a higher threshold for antagonism.
Fig. 7: Activation properties of 6F-CD3ζ TCRs are accurately predicted by a new model of KPR with negative feedback.
Fig. 8: OTI-6F(i) CD8+ T cells exhibit higher cytotoxicity toward tumors expressing low-affinity antigens.

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All data are available in the main text and supplementary materials. All materials described in this article are available upon request and may require an NIH material transfer agreement. Source data are provided with this paper.

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Acknowledgements

We thank L. Samelson (National Cancer Institute (NCI)) and K. Pfeifer (NICHD) for critical reading of the manuscript. This work was supported by the NIH and NCI intramural research programs (Project number: 1ZIAHD001803-29 to P.E.L). Research reported in this publication was supported by the Office of Clinical Research BtB Program Funds-award # 996369 (PEL).

Author information

Author notes

  1. John Davies

    Present address: Department of Safety Assessment, Genentech, Inc., San Francisco, CA, USA

  2. Christian S. Hinrichs

    Present address: Duncan and Nancy MacMillan Cancer Immunology and Metabolism Center of Excellence, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA

  3. These authors contributed equally and are listed alphabetically: Sooraj Achar, François X. P. Bourassa, John Davies.

Authors and Affiliations

  1. Hematopoiesis and Lymphocyte Biology Section, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, Bethesda, MD, USA

    Guillaume Gaud, Teri Hatzihristidis, Seeyoung Choi, Jan Lee & Paul E. Love

  2. Immunodynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA

    Sooraj Achar & Grégoire Altan-Bonnet

  3. Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK

    Sooraj Achar

  4. Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada

    François X. P. Bourassa & Paul François

  5. Department of Physics, McGill University, Montréal QC, Canada

    François X. P. Bourassa

  6. Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA

    John Davies & Christian S. Hinrichs

  7. Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA

    Taisuke Kondo & Naomi Taylor

  8. Viral Immunology & Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA

    Selamawit Gossa & Dorian B. McGavern

  9. National Institutes of Health Library, Office of Research Services, National Institutes of Health, Bethesda, MD, USA

    Paul Juneau

  10. Mila Québec, Montréal, Quebec, Canada

    Paul François

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Contributions

G.G., J.D., S.A., F.X.P.B., C.S.H., P.F., D.B.M., P.J., N.T., G.A.-B. and P.E.L. conceptualized the study. G.G., J.D., S.A., F.X.P.B., P.F., D.B.M., G.A.-B. and P.E.L. devised the methodology. G.G., J.D., S.A., F.X.P.B., T.H., S.C., T.K., S.G. and J.L. carried out experiments. G.G., C.S.H., P.F., D.B.M., G.A.-B. and P.E.L. acquired the funding. G.G., G.A.-B. and P.E.L. administered the project. C.S.H., P.F., D.B.M., G.A.-B. and P.E.L. supervised the study. G.G. and P.E.L. wrote the original draft. G.G., J.D., S.A., F.X.P.B., C.S.H., P.J., P.F., N.T., G.A.-B. and P.E.L. reviewed and edited the draft.

Corresponding author

Correspondence to Paul E. Love.

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Competing interests

G.G., J.D., C.S.H. and P.E.L. are inventors on an NIH patent using ITAM-mutated CD3ζ to enhance the function of cytotoxic T cells and other immune cells; Patent #: 63/113,428. The remaining authors declare no competing interests.

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Nature Immunology thanks Stephen Jameson and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Primary Handling Editor: S. Houston in collaboration with the rest of the Nature Immunology editorial team.

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Extended data

Extended Data Fig. 1 6Y and 6F CD3ζ protein variants are expressed at the same level in peripheral T cells and 6Y and 6F(i) mice have similar phenotypes.

CD8+ T Cells from 6Y/6Y dLck-Cre- [6Y] and 6Y/6Y dLck-Cre + [6F(i)] mice were analyzed for CD3ζ expression by: (a) Intracellular staining with anti-CD3ζ and FACS acquisition (representative plot on left, summary graph on right), or (b) Western blot with anti-CD3ζ after cell lysis using the indicated detergents. (c) Surface TCRβ levels (MFI) were determined by antibody staining and FACS (representative plot on left, summary graph on right). d-g, Phenotype of 6Y/6Y OX40-Cre- [6Y] and 6Y/6Y OX40-Cre + [6F(i)] mice. (d) Flow cytometry analysis of CD4/8 populations in Thymus, Spleen and Lymph nodes. (e) Flow cytometry analysis of naïve/memory and Treg populations in Spleen. (f,g) Plots showing the percentage of indicated cell populations in the thymus (f) and Lymph node/Spleen (g) of 6Y and 6F(i) mice. Data are expressed as mean value ± SD). Plots shown are representative of at least three experiments with two mice per genotype.

Extended Data Fig. 2 Phenotype of OTI 6Y/6Y dLck-Cre- [OTI-6Y] and OTI 6Y/6Y dLCK-Cre + [OTI-6F(i)] mice.

(a,b) Flow cytometry analysis of Spleen and Lymph nodes (a) or thymus (b). Data are representative of at least three experiments with two mice per genotype. (c) Intracellular staining showing expression of CD3ζ-6F-Myc in double positive (CD4+ CD8+ ; DP), immature (CD24High TCRβlow) and mature (CD24Low TCRβHigh) CD8 SP thymocytes and peripheral CD8+ T cells from OTI-6Y and OTI-6F(i) mice. (d) Cellularity of thymus, or pooled axillary, brachial and inguinal lymph nodes (LN) and spleen of OTI-6Y and OTI-6F(i) mice. Data are expressed as mean value ± SD (n = 6 mice from three independent experiments). (e) CD8+ T cells from OTI 6Y/6Y dLck-Cre- [6Y] and OTI 6Y/6Y dLck-Cre + [OTI-6F(i)] mice were analyzed for key threshold TCR signaling regulators by FACS analysis. Data are expressed as mean value ± SD (n = 4 mice from two independent experiments). (f) CD5, CD44, CD25 and CD69 activation marker expression, and CTV dilution (proliferation), by/of peripheral naive OTI-6Y and OTI-6F(i) CD8+ T cells stimulated with increasing amounts of anti-CD3 (μg/ml) alone (left panel) or in combination with anti-CD28 (1 µg/ml) (right panel). Data are expressed as mean value ± SD (n = 3 biological replicates). Data representative of three independent experiments. (g) OTI WT [OTI + / + ], OTI 6Y/6Y dLck-Cre- [OTI-6Y] and OTI-6Y/6Y dLck-Cre + [OTI-6F(i)] T cells were co-cultured with APC pulsed with 10−8 M or 10−10 M of the indicated peptide for 24 h and the expression of the indicated activation markers was analyzed by FACS. Data are expressed as mean value ± SD (n = 3 biological replicates). Data representative of two independent experiments. *P < 0.05, **P < 0.01, ***P < 0.001, ns not significant.

Extended Data Fig. 3 6F-CD3ζ-expressing CD8+ T cells have a lower threshold of activation by low affinity antigens. Related to Fig. 2.

CD8+ T cells from OTI 6Y/6Y dLck-Cre- [OTI-6Y] and OTI 6Y/6Y dLck-Cre + [OTI-6F(i)] mice were co-cultured with APC pulsed with 10−6 M of the indicated peptide and accumulation of: (a) IL-2, (b) IFNγ, (c) IL-6, or (d) TNFα was assessed in the culture supernatants at the indicated times. Heatmaps of cytokine expression are shown on top. Bottom, Graphs of cytokine measurements are shown as Log10(cytokine/ LOD), where LOD is the limit of detection. Data are represented as mean ± SEM. Statistical significance determined by two-way ANOVA corrected with Sidak test for multiple comparison. Data are representative of 8 independent experiments. (e) OTI 6Y/6Y [OTI-6Y] and OTI 6Y/6Y Ert2-Cre + [OTI-6F(i)] CD8+ T cells were treated in vitro with 4-OH tamoxifen for 48 hr before stimulation experiments. T cells were co-cultured with APC pulsed with 10−6 M of the indicated peptide and accumulation of IL-2, IFNγ, IL-6 or TNFα was assessed in the culture supernatants. Graphs of cytokine measurements are shown as mean of logarithm of concentrations over the whole time-course of the experiment, normalized by the lower limit of detection (LOD) in supernatant. N = 3 biological replicates from three independent experiments. Data are represented as mean ± SEM. Statistical significance determined by two-way ANOVA corrected with Sidak test for multiple comparison. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns, not significant.

Extended Data Fig. 4 The enhancing effect of 6F-CD3ζ on TCR signaling in response to low affinity ligands is diminished when the ligand concentration (avidity) is increased. Related to Fig. 2.

4-OH tamoxifen treated OTI 6Y/6Y [OTI-6Y] and OTI 6Y/6Y Ert2-Cre + [OTI-6F(i)] CD8+ T cells (a) or OTI 6Y/6Y [OTI-6Y], OTI 6Y/6Y dLck-Cre + [OTI-6F(i)], and germline OTI 6F/6F [OTI-6F] CD8+ T cells (b) were stimulated with APC pulsed with the indicated concentration of peptides and analyzed for cytokine production in the supernatant (a) or CD69 surface expression by FACS (b). Statistical significance determined by unpaired two-sided t-test analysis (a) or two-tailed ANOVA test analysis (b). Data are represented as Mean ± SEM. N = 3 biological replicates, Data representative of three independent experiments. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns, not significant. Data are from three independent experiments. c, d, e, 6F-CD3ζ-expressing T cells have a lower threshold of activation toward low affinity antigens. Related to Fig. 3. (c) Proliferation of CD8+ T cells from OTI 6Y/6Y dLck-Cre- [OTI-6Y] and OTI 6Y/6Y dLck-Cre + [OTI-6F(i)] mice co-cultured for 72 h with APC pulsed with 10−6 M of the indicated peptide assessed by Cell Trace Violet (CTV) dilution. Summary of experiments are shown in the graph below. N = 5 biological replicates from 2 independent experiments. Data are represented as Mean ± SEM. Statistical significance determined by two-way ANOVA corrected with Sidak test for multiple comparison. (d), OTI CD8+ T cells from OTI 6Y/6Y [OTI-6Y] or OTI 6Y/6Y dLck-Cre + [OTI-6F(i)] mice were stimulated for 2 minutes with peptide-pulsed APCs. Graph represents the percentage of pZAP-70 (Y319), pLAT (Y171) or pErk1/2 (T202/Y204) positive cells from intracellular staining. Data were analyzed by unpaired t-test (two tailed) and are represented as mean ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. (e), OTI-6Y and OTI 6Y/6Y Ert2-Cre + [OTI-6F(i)] CD8+ T cells were treated in vitro with 4-OH tamoxifen for 3 days, stimulated for 2 min with the indicated Kb peptide-tetramers, lysed and analyzed by PAGE and immunoblot with the indicated antibodies. Data are representative of three independent experiments.

Extended Data Fig. 5 Analysis of the cytokine release profile of germline OTI-6F CD8+ T cells over a 72 hr time course. Related to Fig. 4.

(a) Distribution of cytokine secretion levels of effector OTI-6Y or OTI-6F (germline) CD8+ T cells pre-stimulated with 10-6 M-6 N4 antigen + APCs for 6 days then re-stimulated with APC + 10-6 M antigens of varying affinities.(b) Mutual information (antigen classes) between antigen quality and all secreted cytokines for each genotype. While OTI-6Y T cells can distinguish more than four classes of antigen across the 6 peptide affinities tested, OTI-6F T cells only distinguish two. Data are expressed as MI estimator ± SD.(c) Summary plots of cytokine secretion showing scaled mean over time. Data are represented as mean ± SD. (d) Mutual information (antigen classes) between antigen quality and each secreted cytokine for each genotype. Data are expressed as MI estimator ± SD. ([n = 14 OTI-6Y (OTI 6Y/6Y) or n = 10 OTI-6F (OTI 6F/6F) biological replicates].

Extended Data Fig. 6 Analysis of the cytokine release profiles of OTI-6F(i) CD8+ blasts restimulated with 10-6 M peptide (a-c) or 10-9 M peptide (d-f) over a 72 h time course. Related to Fig. 4.

(a-c), OTI-6Y (OTI 6Y/6Y dLckCre-) and OTI-6F(i) (OTI 6Y/6Y dLckCre+) CD8+ T cells were co-cultured with APC pulsed with 10 −6 M N4 peptide for 6 days then re-stimulated with APC + 10-6 M antigens of varying affinities. (a) Distribution of cytokine secretion levels. Data are represented as mean ± SD. (b) Summary plots of cytokine secretion showing scaled mean over time. (c) Mutual information (antigen classes) between antigen quality and each secreted cytokine for each genotype. N = 3 biological replicates. Data are expressed as MI estimator ± SD.(d-f) OTI-6Y and OTI-6F(i) CD8+ T cells were co-cultured with APC pulsed with 10 −6 M N4 peptide for 6 days then re-stimulated with APC + 10-9 M antigens of varying affinities. (d) Distribution of cytokine secretion levels. Data are represented as mean ± SD. (e) Summary plots of cytokine secretion showing scaled mean over time. (f) Mutual information (antigen classes) between antigen quality and each secreted cytokine for each genotype. N = 3 biological replicates. Although MI/Antigen class plots are similar for OTI-6Y and OTI-6F(i) T cells due to the enhanced response of OTI-6F(i) T cells to low affinity ligands, OTI-6F(i) T cells exhibit reduced discrimination of mid-high affinity ligands. Data are expressed as MI estimator ± SD.

Extended Data Fig. 7 Activated and expanded 6F-CD3ζ-expressing CD8+ T cells exhibit a lower threshold of activation toward low affinity peptides. Related to Fig. 8.

OTI-6Y [OTI 6Y/6Y-Ert2-cre-]; OTI-6F(i) [OTI 6Y/6Y Ert2-Cre+]; and OTI-6F germline [OTI 6F/6F] T cells were treated in vitro with 4-OH tamoxifen for 48 hr then activated in vitro with 0.5x10-6 M N4 peptide for 6 days before secondary stimulation experiments. (a), FACS analysis showing CD62L vs CD44 surface staining, or (b), CD5 and TCRβ surface staining (Mean Fluorescence Intensity; MFI) of OTI CD8+ T cells of the indicated genotypes after in vitro activation and expansion. (c,d) Activated and expanded OTI CD8 T cells were re-stimulated with APC pulsed with the indicated peptides and analyzed by FACS for CD25 surface expression (c) or IFNγ expression (d) by intracellular staining. Bar graph plots show MFI of CD25 (left) or % IFNγ+ cells (right) from experiments shown in (c) and (d), respectively. Statistical significance determined by unpaired t-test analysis. *p < 0.05, **p < 0.01, ***p < 0.001,****p < 0.0001, ns, not significant. Data are representative of at least two experiments. (e) OTI CD8+ T cells of the indicated genotypes were treated in vitro with 4-OH tamoxifen for 48 h and activated with 0.5x10-6 M N4 peptide for 6 days before experiments. OTI-6Y [OTI 6Y/6Y Ert2-cre-]; OTI-6F(i) [OTI 6Y/6Y Ert2-cre+]. Shown are in vitro killing assays of OTI CD8+ T cells from the indicated mice against B16 F10-N4 (left) or B16 F10-V4 (right) target cells at the indicated effector-to-target ratios by xCELLigence RTCA (Agilent). Data are represented as mean ± SD.

Extended Data Fig. 8 6F-CD3ζ-expressing CD8+ T cells exhibit higher cytotoxicity toward tumor cells expressing low affinity (V4) ligand. Related to Fig. 8.

(a) Plot showing individual tumor measurements related to Fig. 8b. (b) C57B6 mice were injected with pre-activated (0.5x10-6M N4 peptide) OT1-6Y or OTI-6F CD8+ T cells 7 days after B16F10-V4 melanoma implantation. Results shown are representative of 3 experiments. Top, measurement of the size of B16F10-N4 or B16F10-V4 tumors implanted into C57B6 mice. Bottom, survival curves of experiment shown above. Data are represented as mean ± SD (c) Left, Rag2−/− mice that were injected with pre-activated (0.5x10-6M N4 peptide) OT1-6Y or OTI-6F CD8+ T cells 7 days after B16F10 melanoma implantation. Right, survival curves of experiments shown on left. Results shown are representative of 3 experiments. Data are represented as mean ± SD. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, ns, not significant.

Extended Data Fig. 9 Retroviral (RV) transduction of 6F-CD3ζz into WT (+/+) OTI CD8+ T cells enhances TCR-mediated anti-tumor responses. Related to Fig. 8.

(a-c) WT (+/+) OTI CD8+ T cells stimulated with N4 peptide (0.5x10-6M) and APCs were transduced with retroviruses (RV) expressing 2A-epitope tagged 6Y-CD3ζ (6Y) or 6F-CD3ζ (6F) before addition to tumor cell cultures. (a) Transduced OTI T cells were analyzed by FACS for the indicated markers. RV-encoded LNGFR was used to assess transduction efficiency. (b), Transduced OTI CD8+ T cells were analyzed by immunoblot for the presence of TCR associated 2A-tagged RV-encoded 6Y or 6 F CD3ζ after immunoprecipitation with anti-TCRβ and PAGE to confirm incorporation of transduced ζ chains into the TCR. IP-immunoprecipitated, CL-cell lysate. Data are representative of two independent experiments.(c) Plot showing individual tumor measurements related to Fig. 8d.

Extended Data Fig. 10 OTI CD8+ T cells heterozygous for the CD3ζ-6F allele [6F/+(i)] display an intermediate phenotype compared to OTI-6Y and OTI-6F(i) T cells. Related to Fig. 8.

(a) CD8+ T cells from OTI 6Y/6Y dLck-Cre- [OTI-6Y], OTI-6Y/+ dLck-Cre + [OTI-6F/+(i)] and OTI-6Y/6Y dLck-Cre + [OTI-6F(i)] mice were co-cultured with APC pulsed with 10−8 M of the indicated peptide and accumulation of cytokines was assessed in the culture supernatants at 16 h. N = 3 biological replicates. Data are represented as mean ± SD. Statistical significance determined by two-way ANOVA corrected with Sidak test for multiple comparison. Data are representative of 2 independent experiments. (b) Ratio of IL-2 and IFNγ concentrations (‘antagonism ratio’) for all agonist (N4; 10−8 M) / antagonist (V4, G4, E1; 10−6 M) combinations. N = 3 biological replicates. Data are represented as mean ± SD. Data are representative of 2 independent experiments. (c) Expression of CD3ζ with mutation of the ITAM tyrosines (Y) to phenylalanine (F) or alanine (A) or deletion of the ITAMs (truncated) enhances OTI CD8+ T cell cytotoxic responses. OTI (+/+) CD8+ T cells were stimulated with N4 peptide then transduced with retroviruses expressing 6Y, 6F, 6A (where all 6 ITAM tyrosines have been mutated to alanine) or a truncated CD3ζ chain lacking the 3 ITAMs. Shown are in vitro tumor killing assays at 10:1, 5:1 or 2.5:1 effector-to-target ratios by xCELLigence RTCA (Agilent). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, ns, not significant.

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Unprocessed immunoblots for Figs. 1, 3 and 5 and Extended Data Figs. 4 and 9.

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Statistical source data for Figs. 1, 2, 3, 6 and 8 and Extended Data Figs. 1, 2, 3, 4, 8 and 10.

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Gaud, G., Achar, S., Bourassa, F.X.P. et al. CD3ζ ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides. Nat Immunol 24, 2121–2134 (2023). https://doi.org/10.1038/s41590-023-01663-2

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