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1 a! T Cells! TKO! B Cells! TKO! b! CD4! CD8! Tbk1-TKO! c! DN cells (%)! DP cells (%)! CD4 + SP cells (%)! TKO! TKO! TKO! TKO! CD8 + SP cells (%)! CD4 + T Cells (X1 6 )! d! 6-week old mice! e! 4-month old mice! 2 15! 1 5! CD8 + T Cells (X1 6 )! 1 8! 6 4! 2! CD4 + T Cells (X1 6 )! 25! 2 * 15! 1 5! * * CD8 + T Cells (X1 6 )! 15! 1 5 * * cell! Medium! α-cd3+α-cd28! f! TKO! 2 Annexin V! Supplementary Fig. 1. Thymocyte development and peripheral T-cell distribution in WT and Tbk1-TKO mice. (a) Immunoblot analysis showing the specific ablation of Tbk1 in T cells, but not in B cells, of Tbk1-TKO mice. (b,c) Flow cytometric analysis of thymocytes from WT and Tbk1-TKO mice (6 wk old). Numbers in quadrants indicate the percentage of CD4 CD8 double-negative (DN), CD4 + CD8 + double-positive (DP), CD4 + single-positive (SP), and CD8 + SP thymocytes. Data are representative plot (b) and mean ± SD values (c) of 3 mice per group. (d,e) CD4 + and CD8 + T-cell numbers from spleen, peripheral lymph nodes (pln), mesenteric lymph nodes (mln), bone marrow (BM), peripheral blood (PBL) of 6-week old mice (wt=7,ko=6) (d) and 8-month old mice (wt=4, ko=3) (e). (f) Flow cytometry analysis of apoptosis, based on annexin V staining, of WT or Tbk1-TKO CD4+ T cells incubated for 48 with medium or anti-cd3 plus anti-cd28. *P<.5;, non-significant.

2 a! WT- Tbk1- c! CD4! b! CD44! WT- CD62L! WT- Tbk1- d! CD8! Tbk1- DN cells (%)! WT-! CD4 naïve (%)! DP cells (%)! Tbk1-! WT-! *! 6 *! Tbk1-! CD4 memory (%)! 4 2 CD4 + SP cells (%)! WT-! Tbk1-! WT-! Tbk1-! WT-! CD8 + SP cells (%)! Tbk1-! WT-! Tbk1-! Supplementary Fig. 2. Inducible ablation of TBK1 in adult mice impairs T-cell homeostasis without influencing thymocyte development. (a) Immunoblot analysis of TBK1 in T cells isolated from tamoxifen-treated Tbk1 +/+ Cre-ER (WT-ER) or Tbk1 fl/fl Cre-ER (Tbk1-ER) mice (after two weeks of tamoxifen injection). (b) Flow cytometric analysis of the percentage of memory (CD44 hi CD62L lo ) and naïve (CD44 lo CD62L hi ) CD4 + T cells in the spleen of WT and Tbk1-ER mice. Data are representative plot (left) and mean ± SD values (right) of multiple mice (each circle represents a mouse). (c,d) Flow cytometric analysis of the thymocyte subpopulations from WT and Tbk1-ER mice after weeks after tamoxifen injection. Data are representative plot (c) and mean ± SD values (d). *P<.5;, non-significant.

3 Tbk1-TKO! Th IFN-γ IL-17! IFN-γ Th1! IL-17! Th17! IL-17! IFN-γ Supplementary Fig. 3. TBK1 deficiency promotes Th1 differentiation in vitro. Naive CD4 + T cells isolated from WT and Tbk1-TKO mice were stimulated for 72 hours with platebound anti-cd3 (5µg/ml) and anti-cd28 (1µg/ ml) under Th, Th1, or Th17 conditions followed by flow cytometry to measure the frequency of IFN-γ-producing Th1 cells and IL-17-producing Th17 cells

4 a! CD4 + T Cells (X1 6 )! CD4 + T Cells! CD8 + T Cells! 4! B Cells! CD8 + T Cells (X1 6 )! 1. n.d! n.d! n.d! Med LN! Lung! Med LN! Lung! Med LN! Lung! B22 + Cells (X1 6 )! 3! 2! 1! WT-ctrl! TKO-ctrl! WT-flu! TKO-flu! b! c! Ratio to initial body weight! 1.2!.9!.6!.3! Day After Infection! TKO! Cytokine (ng/ml)! 4! 3! 2! 1! TKO! IFN-γ IL-12 p4 Supplementary Fig. 4. TBK1 deficiency does not affect immune responses against influenza viral infection. Flow cytometry analysis of the indicated cell types in the mediastinal lymph nodes (Med LN) and lung (a), bodyweight loss (b), and ELISA of cytokine level in the bronchoalveolar lavage fluid (c) of WT or Tbk1-TKO (TKO) mice infected intranasally with influenza (flu) virus PR8 for 8 days. Data are presented as mean ± s.d. (n=4).

5 2. Itga4 1. Itgb1 1. Ninj1 1. cxcr ccr5 1. ccr TKO! Supplementary Fig. 5. TBK1 is dispensable for the expression of integrin. QPCR analysis of relative gene expression in freshly isolated CD4 + T cells from draining LN of WT and Tbk1-TKO mice induced with EAE for 18 days.

6 a! Total! TKO! P-p38! p38! P-ERK1/2! ERK1/2! b! Tbk1-! IKKε-! TKO! KO P- AKT! S6! c! Naïve! Memory! TKO! TKO! P- AKT! S6! d! WT-! Tbk1-! P- AKT! S6! e! Relative AKT mrna! naive TKO! memory f! HA- GFP! FLAG-! Supplementary Fig. 6. TBK1, but not IKKε, negatively regulates AKT-mTORC1 signaling. (a-c) Immunoblot (IB) analysis of the indicated phosphorylated (P-) and total proteins in freshly isolated total CD4 + T cells (a,b) or FACS sorted naïve and memory CD4+ T cells (c) from WT, Tbk1-TKO (TKO), and IKKε-KO mice. (d) IB analysis using freshly isolated CD4 + T cells of WT-ER and Tbk1-ER mice after two weeks of tamoxifen injection. (e) QPCR analysis of relative AKT expression in freshly isolated naïve and memory CD4 + T cells from WT and Tbk1-TKO mice. (f) IB analysis of the indicated proteins using HEK293T cells transfected with an empty vector or the same vector encoding FLAG-tagged TBK1 or its catalytically inactive mutant (K38A), along with vectors encoding GFP and HA-tagged AKT. A non-specific band, detected by the FLAG antibody, was indicated by an arrowhead (bottom panel).

7 a! shrna! C! #1! #2! P- S6! P-Foxo1! Foxo1! Relative mrna (fold)! b! 1. Control shrna! TBK1 shrna! * * * c! d! Migrating T Cells (X1 3 )! 25! *! 2 15! 1 5! C! sh shrna! Migrating T Cells (X1 3 )! 3 *! 2 1 C! AM! Inhibitor! e! Tbk1! 3! 2! 1! *! C! MS! Supplementary Fig. 7. TBK1 regulates AKT-mTORC1 signaling and homing gene expression in human T cells. (a) IB analysis of phosphorylated (P-) and total proteins in human PBMCs transduced with a lentiviral vector (plko.1) encoding a control luciferase shrna (C) or two different TBK1 shrnas. (b) QPCR analysis of the indicated genes using human PBMCs transduced with control (C) or TBK1 shrnas. (c,d) In vitro migration assay of activated human CD4 + T cells that were transduced with a control (C) or TBK1-specific shrna or treated with DMSO (C) and a TBK1 inhibitor, amlexanox (AM, 25 µm). The number of CD4 + T cells migrating through a human brain microvascular endothelial cell monolayer was counted as migrating T cells, and data are representative of three independent experiments performed in duplicates. (e) QPCR analysis of Tbk1 expression in human PBMCs of healthy donors (C, n=13) or MS patients (MS, n=15). *P<.5.

8 Fig. 1a! P- α-cd3 +! α-cd28! PMA + Iono! 7.5!15! 7.5!15!(min)! Fig. 1c! PMA +! Jurkat! JPM5.6! Iono (min)! 7.5!15!7.5!15! TBK1 KA! P-GST-IRF3! J.SVT35! JM4.5.2! 7.5!15!7.5!15! IKKε KA! P-GST-IRF3! Fig. 1b! PMA +! Iono (min)! TBK1 KA! P-GST-IRF3! Carma1-! KO! 7.5!15!7.5!15! NEMO-! TKO! 7.5!15!7.5!15! IKKβ- TKO! 7.5!15!7.5!15! IKK KA! P-GST-IκBα IKKε KA! P-GST-IRF3! IKK KA! P-GST-IκBα Supplementary Figure 8. Full scans of blots for figures 1a-1c.

9 Fig. 5a! TKO! P- P-Foxo1! Foxo1! P-S6K1! S6K1! Fig. 5d! Fig. 5b! P- TKO! α-cd3 + α-cd28! 7.5!15!7.5!15! min! Fig. 5e! α-cd3 +! DMSO! MRT6737! α-cd28 (h)! 1! 2! 4! 6! 1! 2! 4! 6! Fig. 5c! Fig. 5f! P- P-S6K1! S6K1! FLAG-! EAE! TKO! DMSO! MG132!! K38A!! K38A! Ub-! Fig. 5g! HA- FLAG- TBK1!+!! +!!+!!+! HA- GFP! FLAG-! Supplementary Figure 9. Full scans of blots for figures 5a-5h. Fig. 5h! FLAG-! HA- GFP! HA-

10 Fig. 5i! Rapa-! DMSO! mycin! Fig. 6d! sfig. 1a! T Cells! B Cells! Fig. 5j! P- AKT! S6! P-Foxo1! TKO! sfig. 2a! TKO! P- Foxo1! Total! sfig. 6a! TKO! P-p38! p38! P-ERK1/2! ERK1/2! sfig. 6b! Tbk1-! IKKε-! TKO! KO P- Supplementary Figure 1. Full scans of blots for figures 5i, 5j, 6d, and supplementary figures 1a and 2a.

11 sfig. 6c! P- Naïve! TKO! Memory! TKO! sfig. 6d! P- WT-! Tbk1-! sfig. 6f! sfig. 7a! P- shrna! C!#1!#2! shrna! C!#1!#2! HA- GFP! FLAG-! P-Foxo1! Foxo1! Supplementary Figure11. Full scans of blots for supplementary figures 6c, 6d, 6f, and 7a.

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