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1

Cytokine Production in Crtam-Deficient T Cells

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LN CD4+ T cells from WT and Crtam−/− mice were enriched using a CD4+ T cell isolation kit (Miltenyi Biotec). 2 × 105 cells were activated with plate-bound anti-CD3 (10 µg/ml) and anti-CD28 (2 µg/ml) under polarizing TH1 conditions, i.e., recombinant IL-2 (PeproTech), mIL-12 (PeproTech), and anti–mouse IL-4 mAb (11B11), or TH17 conditions, i.e., recombinant mIL-6 (PeproTech), hTGFb, mIL-23, mAb anti-IL-4 (11B11), and anti–IFN-γ (RUGA2) for 5 d (primary stimulation). For the secondary stimulation, T cells were washed, counted, and 2 × 105 cells were restimulated with plate-bound anti-CD3 (10 µg/ml) and anti-CD28 (2 µg/ml) without added cytokines or antibodies for 2 more days. Cells were analyzed for cytokine production by intracellular staining either after 5-d stimulation or 2-d restimulation. Supernatants were also collected at these times, and IFN-γ and IL-17 concentrations determined by cytometric bead array (BD).
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2

Generation and Characterization of Gimap5 Knockout Mice

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All experiments were performed according to US National Institutes of Health guidelines and were approved by the IACUC of The Cincinnati Children’s Hospital. C57BL/6J mice were obtained from Jackson. Deletion of Gimap5 in Gimap5flox/floxCd4cre-ert2 mice was induced by the administration of tamoxifen chow (40mg/kg body weight; Harlan Laboratories Teklad Diets). Gimap5sph/sph mice were generated as previously described (6) and bred in-house in the vivarium of Cincinnati Children’s Hospital. All mice were maintained under specific pathogen-free conditions.
All antibodies used for flow cytometry were purchased from eBioscience or Biolegend unless otherwise noted. Purified α-mouse-CD3 (17A2) and α-mouse-CD28 (37.51) antibodies (Biolegend) were used for mouse T cell activation. A fixable viability stain was purchased from eBioscience. 7-AAD was purchased from BD. PMA, ionomycin, and Brefeldin A were obtained from Sigma. αIFNγ (XMG1.2) and mIL-23 were obtained from eBioscience. TGFβ1, mIL-4, and hIL-2 were purchased from Miltenyi Biotech. αIL-4, IL-6, and mIL-1β, mIL-12, and TGFβ3 were obtained from PeproTech.
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3

Murine SON-1210 Cytokine Fusion Protein

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The murine version of SON-1210, which has mouse (m) and human (h) cytokine sequences in the respective payload positions (mIL12-FHAB-hIL15), was produced in CHO cells using shake flasks. The monofunctional mIL12-FHAB, hIL12-FHAB, and hIL15-FHAB molecules, as well as mIL-12, hIL-12, hIL-15, and their His-tagged versions were produced in the same way (31 (link)). The SON-1210 clinical manufacturing process was performed using continuous perfusion during a 15-day manufacturing process. Purification was accomplished using multiple chromatography steps, resulting in a Good Manufacturing Process (GMP) product quality that is suitable for human use. All molecules were formulated in histidine-based buffer containing trehalose, DTPA, and polysorbate 20 at pH 7.3. The diluent used as the negative control was identical to the formulation buffer. Some recombinant human IL-12 (hIL-12), murine IL-12 (mIL-12), and human IL-15 (hIL-15) reference material and reagents used in these studies were purchased from Peprotech (Cat# 200-12, Cat# 200-15, respectively), and R&D Systems (Cat# 419-ML-010/CF).
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4

Polarization of Murine T Helper Cells

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For in vitro T cell assays, naïve (CD4+ CD25 CD44Lo CD62LHi) T cells were purified by bead enrichment and/or flow cytometric sorting from spleens and lymph nodes from the indicated strains of mice prior to stimulation with plate bound anti-CD3 (2.5 µg/ml; UCSF Monoclonal Antibody Core) and anti-CD28 (2 µg/ml; UCSF Monoclonal Antibody Core). In addition, mIL-12 (20ng/ml, Peprotech) and anti-IL-4 (10µg/ml, 11B11:Tonbo) were used for TH1 polarization, while hTGFβ (5ng/ml, Peprotech), mIL-6 (20ng/ml, Peprotech), anti-IL-4 (10µg/ml) and anti-IFNγ (10µg/ml, XMG1.2, UCSF hybridoma core) were used for TH17 polarization. In selected experiments, T cells were labeled with 3 mM CFSE (Invitrogen). siRNA mediated reduction of RIPK3 in Jurkat I9.2 cells (ATCC) was performed using one pulse of 2200 V and 20 ms, using Neon Transfection System (Invitrogen) according to manufacturer’s instructions.
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5

Polarization of Murine T Helper Cells

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For in vitro T cell assays, naïve (CD4+ CD25 CD44Lo CD62LHi) T cells were purified by bead enrichment and/or flow cytometric sorting from spleens and lymph nodes from the indicated strains of mice prior to stimulation with plate bound anti-CD3 (2.5 µg/ml; UCSF Monoclonal Antibody Core) and anti-CD28 (2 µg/ml; UCSF Monoclonal Antibody Core). In addition, mIL-12 (20ng/ml, Peprotech) and anti-IL-4 (10µg/ml, 11B11:Tonbo) were used for TH1 polarization, while hTGFβ (5ng/ml, Peprotech), mIL-6 (20ng/ml, Peprotech), anti-IL-4 (10µg/ml) and anti-IFNγ (10µg/ml, XMG1.2, UCSF hybridoma core) were used for TH17 polarization. In selected experiments, T cells were labeled with 3 mM CFSE (Invitrogen). siRNA mediated reduction of RIPK3 in Jurkat I9.2 cells (ATCC) was performed using one pulse of 2200 V and 20 ms, using Neon Transfection System (Invitrogen) according to manufacturer’s instructions.
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6

In Vivo T Cell Activation Assay

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All animal studies were performed according to National Institutes of Health (NIH) guidelines for the use and care of live animals and were approved by the Animal Care and Use Committees of the National Cancer Institute (NCI) under the protocol 20-073. C57BL/6 CD4-Cre transgenic, RAG−/− mice and Ifngr KO (JAX:003288) mice were obtained from the Jackson Laboratory and bred in our institute animal facility under specific pathogen–free conditions. Sptlc1foxl/flox mice were generated in our laboratory as previously described (34 (link)). Sptlc1foxl/floxCD4-Cre (KO) conditional KO mice were generated by crossing Sptlc1floxl/flox mice to CD4-Cre transgenic mice. Sptlc1foxl/flox or Sptlc1+/+CD4-Cre were used as control mice (WT). All mice used for experiments were aged 8 to 12 weeks, and both female and male mice were used for experiments. Primers for qPCR were obtained from IDT (Integrated DNA Technologies, USA). Cytokines mIL-4, mIL-12, hTGF-β1, IL-7, and IL-1β were purchased from PeproTech, USA; hIL-2 was obtained from R&D Systems; and IL-6 and IL-23 were purchased from BioLegend, USA. Antibodies for activation and cytokine neutralization were procured from Bio X Cell, USA. All chemicals were purchased from Sigma-Aldrich unless otherwise mentioned.
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7

Isolation and Differentiation of Naive T Cells

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Naive T cells were isolated by sorting CD4+CD25CD62LhiCD44low cells from spleens and lymph nodes (seen gating strategy in Supplementary Fig. 10a), and stimulated with the plate-bound anti-CD3 (clone 17A2; BioXCell, 5 μg ml−1) and anti-CD28 (clone 37.51; BioXCell, 5 μg ml−1) under different cytokine cocktails. The T cells were cultured with anti-IFN-γ (clone XMG1.2; BioXCell, 10 μg ml−1) and anti-IL-4 (clone 11B11; BioXCell, 10 μg ml−1) for Th0 differentiation, mIL-12 (Peprotech; catalog 210-12, 10 ng ml−1) and anti-IL-4 (10 μg ml−1) for Th1 differentiation, mIL-4 (Peprotech; catalog 214-14, 10 ng ml−1) and anti-IFN-γ (10 μg ml−1) for Th2 cell differentiation, hTGF-β1 (R&D Systems; catalog 240-B-010, 2 ng ml−1) with IL-2 (Peprotech; catalog 212-12, 10 U ml−1) for iTreg differentiation. The Th17 differentiation was performed using hTGF-β1 (0.5 ng ml−1) and IL-6 (Peprotech; catalog 216-16, 20 ng ml−1), with or without IL-1β (Peprotech; catalog 211-11B, 10 ng ml−1) and IL-23 (R&D Systems; catalog 1887-ML, 50 ng ml−1) as indicated.
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8

Mouse CD4+ T Cell Differentiation Protocol

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A mouse CD4+ T cell isolation kit (Miltenyi Biotec or BioLegend) was used to isolate CD4+ T cells from LN and spleen. The isolated CD4+ T cells were stimulated for 3 d with plate-bound anti-hamster IgG (12.5 µg/ml), soluble anti-CD3ɛ (145-2C11; BD PharMingen), and anti-CD28 (37.51; BD PharMingen). On day 2, cells were transferred to a fresh plate, without or with the addition of 75 U/ml hIL-2 (Peprotech) and 10 µg/ml anti–mIL-2 (Bio X Cell). The culture conditions for Th0 (no differentiation) were 2.5 µg ConA; for Th1, Th2, and iT reg, 0.5 µg/ml anti-CD3 and 1 µg/ml anti-CD28; and for Th17, 0.25 µg/ml anti-CD3 and 1 µg/ml anti-CD28. For skewing, the following cytokines were added to the culture: Th0, 2.5 µg/ml anti–mIL-4 (Bio X Cell) and 2.5 µg/ml anti–mIFN-γ (Bio X Cell); Th1, 10 ng/ml mIL-12 (PeproTech) and 2.5 µg/ml anti–mIL-4; Th2, 50 ng/ml mIL-4 (PeproTech) and 2.5 µg/ml anti–mIFN-γ; Th17, 0.5 ng/ml mTGFβ, 20 ng/ml mIL-6 (both Peprotech), 2.5 µg/ml anti–mIFN-γ, and 2.5 µg/ml anti–mIL-4; and iT reg, 5 ng/ml mTGFβ, 5 µg/ml anti–mIFN-γ, and 5 µg/ml anti–mIL-4. The cell culture medium was RPMI 1640 for Th1, Th2, and iT reg or IMDM for Th17 cell differentiation and supplemented with 5% FCS, β-mercaptoethanol, and penicillin/streptomycin (Invitrogen).
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9

Generating Th1 and iTreg Cells from TLR2-/- APCs

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APCs were prepared from TLR2−/− disrupted spleens that were T lymphocyte depleted with anti-CD 90.2 beads and LS Magnetic Bead Columns (Miltenyi Biotec) and then gamma irradiated with 2000 rads. For polyclonal activation 0.3 μg/ml CD3ε Abs (clone 2C11, Biolegend) was used or 0.3 μM of OVA peptide (ISQAVHAAHAEINEAGR, Sigma) for OT2 cells. Plate bound stimulation was conducted in 96 well flat bottom plates (Corning) with 0.3 μg/ml CD3ε Abs and soluble 1 μg/ml CD28 Abs (clone CD28.2, Biolegend). Th1 polarization for mouse CD4+ T cells was conducted with 10 μg/ml mIL4 Abs (clone 11B11, Biolegend), 10 ng/ml mIFN-γ (Peprotech) and 10 ng/ml mIL-12 (Peprotech). Th1 polarization for human CD4+ T cells was accomplished with CellXVivo Human Th1 Cell Differentiation Kit (R&D Systems) in accordance with manufacturers recommendations. For iTreg development 0.5 ng/ml of mTGF-β1 (R&D) was used alone or in combination with Th1 polarizing medium.
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10

IL-12 Treatment in Rag2-/- γc-/- Mice

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Rag2−/− γc−/− recipient mice 5 wk after adoptive transfer were injected i.p. with recombinant mIL-12 (Peprotech) at 50 µg/kg body weight. Mice were analyzed 48 h after injection.
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