USP15 stabilizes MDM2 to mediate cancer cell survival and inhibit antitumor T cell responses

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Supplementary Information USP15 stabilizes MDM2 to mediate cancer cell survival and inhibit antitumor T cell responses Qiang Zou 1, Jin Jin 1, Hongbo Hu 1, Haiyan S. Li 1, Simona Romano 1,4, Yichuan Xiao 1, Mako Nakaya 1, Xiaofei Zhou 1, Xuhong Cheng 1, Peirong Yang 2, Guillermina Lozano 2,3, Chengming Zhu 1,3, Stephanie S. Watowich 1,3, Stephen E Ullrich 1,3, Shao-Cong Sun 1,3 1 Department of Immunology and 2 Department of Genetics, The University of Texas MD Anderson Cancer Center, 7455 Fannin Street, Box 902, Houston TX 77030, USA. 3 The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA. 4 Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Naples, Italy

a WT allele E1 E E3 E E2 WT F WT R Insertion E1 site E E3 E E2 Mutant WT F allele OmniBank Vector LTR R ATG Survival (%) h 100 80 60 40 20 0 LTR LTR WT (n=16) KO (n=15) 5 8 11 14 Months 17 20 34.1 33. f CD4 10. 81.8 10.9 81.3 4.5 4.38 CD8 i 48. 2.51 2.6 +/ +/+ / WT allel KO allel +/+ / 78-43 49.1 g CD3 602-1191 1892-220 2504-2839 Actb 26. Usp15 NS 63. CD19 28.9 +/+ / 61.7 250KD 98KD 64KD 50KD CD44 CD44 49.8 51.1 31.9 32.3 CD62L CD62L Supplementary Figure 1. Generation and initial characterization of Usp15 / mice. (a) Schematic picture of Usp15 gene targeting using the OmniBank retroviral gene-trapping technique. (b-d) Genotyping PCR analysis of tail DNAs (b), RT-PCR analysis of the indicated regions of Usp15 cdna in T cells (c), and USP15 immunoblot using T cells (d) of wild-type (WT) (+/+), heterozygous (+/ ), and Usp15 / ( / ) mice. (e) Survival curve of wild-type and Usp15 / (KO) mice. (f) Flow cytometric analysis of thymocytes from wild-type and Usp15 / mice (6 wk old), showing the percentage of CD4 CD8 double negative, CD4 + CD8 + double positive, and the CD4 + and CD8 + single positive populations (n=5 mice/group; showing a representative plot). (g) Flow cytometric analysis of the frequency of CD3 + T cells and the CD19 + B cells in the splenocytes of wild-type and Usp15 / mice (8-12 wk old) (n=5 mice/group; showing a representative plot). (h,i) Flow cytometric analysis of the frequency of naïve (CD44 lo CD62L hi ) and memory (CD44 hi CD62L lo ) populations in the splenic CD4 + T cells from wild-type or Usp15 / mice of 3 (h) or 10 (i) months of age (n=5 mice/group; showing a representative plot). Data are representative of three (f-i) independent experiments.

a NS Ifng mrna 15 10 5 WT EV EV KO USP1 C269A Il4 mrna 4 3 2 1 IFN-γ WT KO EV EV USP15 1.58 4.88 CD Il17 mrna 8 6 4 2 1.8 4.17 Foxp3 mrna 6 4 2 USP15C298A 3 H (c.p.m. 10 4 ) Apoptosis (%) 8 6 4 2 f + α-ifn-γ α-ifn-γ TGF-β (ng/ml) 0. 1. 0. 1. Foxp3 Foxp3 IL-17 CD Supplementary Figure 2. Effect of USP15 deficiency on CD4 + T cell activation and differentiation. (a,b) Rag1 / mice were adoptively transferred with wild-type (WT) or Usp15 / bone marrow cells transduced with a GFP-expressing lentiviral empty vector (EV) or the same vector encoding USP15 or a catalytically inactive USP15 mutant (C298A). GFP + thymocytes (a) and splenic naïve CD4 + T cells (b) were sorted from the indicated chimeric mice and subjected to USP15 IB (a) and intracellular IFN-γ staining following stimulation with anti-cd3 plus anti- CD28 for 72 h (b) (n=3 mice/group; showing a representative plot). (c-e) Naïve CD4 + T cells from wild-type or Usp15 / (KO) mice were stimulated under standard T H 0, T H 1, T H 2, T H 17 or it reg conditions and harvested on day 5 for qrt-pcr (c), proliferation (d), and apoptosis assays (e) (n=3 mice/group). (f) Flow cytometric analysis of T reg cells differentiated for 5 days from wild-type or Usp15-deficient naive CD4 + T cells under T reg cell conditions with different doses of TGF-β in the presence (+) or absence ( ) of an anti-ifn-γ blocking antibody. (g) Flow cytometric analysis of the frequency of Foxp3 + T reg cells among CD3 + CD4 + CD8 - cells in the indicated lymphoid organs of wild-type or Usp15 / mice (5 wk old). Data are presented as a representative plot (left) and a summary graph (right) (n=6 mice/group). All summary graphs are mean ± s.e.m and data are representative of three independent experiments. * P<0.05. 0.9 16.8 42.3 8.19 13. g 0.98 16.7 43. 5.63 13.1 12.3 12.9 Spleen 13. 13.3 MLN PLN Thymus 12.9 13.1 4.2 4.1 CD4 + Foxp3 + cells(%) 1 1

a f Number of CD4 + IFN-γ + T cells per spleen (10 5 ) 3 LM LM g CD11b + cells(%) 8 IFN-γ in CD4 + IFN-γ + T cells (MFI, 10 4 ) 2. 1. 1. 0. CD11c + cells(%) 8 LM LM LM h UI CD45.2 + cells per spleen (10 5 ) 1 8 WT OT-II UI No. of CD4 + T cells/spleen (10 5 ) KO OT-II 1 UI WT KO OT-II OT-II LM i CD45.2 + Foxp3 + cells per spleen (10 3 ) 8 IFN-γ (pg/ml x 10 2 ) 3 1 WT KO OT-II OT-II UI UI WT KO OT-II OT-II LM Supplementary Figure 3. USP15 deficiency enhanced T cell response to listeria infection. (a,b) Flow cytometric analyses of the number of IFN-γ-producing CD4 + T cells (a) and the IFN-γ MFI in the IFN-γ + CD4 + T cells (b) from the spleen of wild-type and Usp15 / mice infected with L. monocytogenes for 6 days (n=5 mice/group). (c-e) Tcrb / Tcrd / mice were reconstituted with 5 10 6 wild-type or Usp15 / (KO) naïve CD4 + T cells in the presence of equal numbers of wild-type CD8 + T cells. After 4 days, the recipient mice were sacrificed for visualizing spleen size (c, n=3 mice/group), flow cytometric analysis of splenic CD4 + T cells (d, n=5 mice/group), and ELISA of serum IFN-γ concentration (e, n=5 mice/group). (f, g) Spleen size (f, n=3 mice/group) and flow cytometric analysis of the frequency of CD11b + monocytes and CD11c + dendritic cells in splenocytes (g, n=5 mice/group) of the reconstituted Tcrb / Tcrd / mice, infected i.v. with 5 10 4 CFU of L. monocytogenes for 4 days. wild-type or Usp15 /, Tcrb / Tcrd / mice reconstituted with wild-type or Usp15 / naïve CD4 + T cells (c-g). (h,i) B6.SJL mice, adoptively transferred with wild-type OT-II or Usp15 / OT-II naïve CD4 + T cells, were either uninfected (UI) or infected for 6 days with OVA-expressing L. monocytogenes (LM) and subjected to flow cytometric analyses of the number of the total transferred T cells (CD45.2 + ) (h) and T reg cells (Foxp3 + CD45.2 + ) (i) in the spleen (n=3 for uninfected and 5 for LM-infected mice). Wild-type OT-II or KO OT-II, B6.SJL mice adoptively transferred with wild-type OT-II or Usp15 / OT-II naïve CD4 + T cells (h, i). UI, uninfected. LM, L. monocytogenes infected. Data are presented as mean ± s.e.m. and representative of at least three independent experiments. * P<0.05; ** P<0.01.

a α-cd3 + WT α-cd3 + WT α-cd28 (min) 1 1 α-cd28 (min) 1 2 1 2 p-lck Lck p-zap70 ZAP70 Actin p-erk ERK p-akt AKT p-s6 S6 Actin 8 6 f 1 h Il2 mrna 6 4 2 TGF-β + α-cd3/cd28 i Ifng mrna 4 2 IL-2 (pg/ml x 10 2 ) 1 TGF-β j IL-2 (pg/ml x 10 2 ) TGF-β (h) 1 1 p-smad2 Smad2 p-smad3 Smad3 IFN-γ (pg/ml x 10 2 ) Actin 1 1 WT g Smad7 mrna α-cd3 + α-cd28 (h) TGF-β + + Lamin B 1. c-myc mrna 1. 0. 1 1 TGF-β (h) EV NFATc2 EV 1. 1 NFATc 8 1.91 3.71 1 1. 10 0. 10 CD 2 48 2 48 1. 3 α-cd3 + α-cd28 (72 h) α-cd3/cd28 (h) α-cd3/cd28 (h) α-cd3/cd28 (h) Supplementary Figure 4. USP15 was dispensable for TCR-proximal signaling and TGF-β signaling in T cells. (a,b) IB analysis of the indicated phosphorylated (p-) and total proteins in the whole-cell lysates of naive CD4 + T cells stimulated with anti-cd3 and anti-cd28 antibodies using a crosslinking protocol. (c,d) wild-type (WT) or Usp15 / naïve CD4 + T cells were stimulated with anti-cd3 plus anti-cd28 for 24 h, starved for 24 h, and then stimulated with TGF-β for the indicated time periods. Cells were subjected to IB (c) or qrt-pcr analysis (d) (n=3 mice/group). (e,f) qrt-pcr analysis of Il2 and Ifng mrna (e) and ELISA of secreted IL-2 and IFN-γ (f) in naïve CD4 + T cells stimulated for 24 h (e) or 48 h (f) (n=3 mice/group). (g) IB analysis using cytoplasmic (CE) and nuclear (NE) extracts of naive CD4 + T cells stimulated with anti-cd3 plus anti- CD28 in the presence (+) or absence ( ) of TGF-β. (h) IB analysis of NFATc2 in EL4 T cells infected with a retroviral vector (EV) or the same vector encoding NFATc2. (i,j) Intracellular staining of IFN-γ (i, n=5 mice/group; showing a representative plot) and ELISA of IL-2 and IFN-γ (j, n=3 mice/group) in the EL4 cells described in h, stimulated as indicated. (k) qrt-pcr analysis of Nfatc2 mrna relative level (normalized to the control Actb) in wild-type or Usp15 / naïve CD4 + T cells, stimulated as indicated (n=3 mice/group). Data in graphs are presented as mean ± s.e.m, and representative of at least three independent experiments. * P<0.05. IFN-γ + α-cd3/cd28 + α-cd3/cd28 IFN-γ (pg/ml x 10 2 ) + α-cd3/cd28 k Nfatc2 mrna NE CE

Il2 mrna Ifng mrna Cdkn1a mrna a IP: α- CE NE CE NE α-cd3 + WT KO UT α-cd3+ HA-U + + α-cd3 + α-cd28 + + CE NE α-cd28 + + + + α-cd28 (h) 3 3 3 3 IB: α- MG132 + + + + USP1 + DMSO IB: α- HLI373 + + + IP: α- NFATc + Lysates p53 IB: α-ha -U NE Lamin B IB: α- Lamin B IB: α- IB: α- Lamin B IB: α- CE DMSO 8 f 1 g 8 HLI373 h MDM2 EV i MDM EV HA- α-cd3 + 10 MDM2 EV α-cd28 (h) 3 3 10 HA- 2.0 4.6 NE 10 Lamin B 3 10 3 3 3 3 WT KO WT KO CE α-cd3/cd28 (h) α-cd3/cd28 (h) CD k DMSO Nutlin-3 α-cd3/cd28 (72 h) j WT KO l 8 1 α-cd3 + EV USP1C298A 8 α-cd3 + DMSO Nutlin-3 α-cd28 (h) 3 3 3 3 α-cd28 (h) 3 3 NE Lamin B NE Lamin B Total 3 3 3 CE NS α-cd3/cd28 (h) Supplementary Figure 5. MDM2 associated with USP15 and regulated TCR/CD28-stimulated NFATc2 activation and cytokine induction in a p53- independent manner. (a) MDM2-USP15 co-ip (upper) and direct IB (lower) assays using cytoplasmic (CE) and nuclear (NE) extracts of wild-type (WT) naïve CD4 + T cells, incubated for 2 h with MG132 either in the absence ( ) or presence of anti-cd3 plus anti-cd28. (b) IB analysis using cytoplasmic (CE) and nuclear (NE) extracts of untreated (UT) wild-type or Usp15 / naïve CD4 + T cells. (c) IB analysis using cytoplasmic (CE) and nuclear (NE) extracts of wild-type naive CD4 + T cells incubated with (+) or without ( ) anti-cd3 plus anti-cd28 for 3 h in the presence of MG132 during the last 2 h. (d) NFATc2 ubiquitination (upper) and IB (lower) analyses using HEK293 cells transfected with the indicated expression vectors. (e,f) IB (e) and qrt-pcr (f, n=3 mice/group) analyses in naïve CD4 + T cells stimulated with anti-cd3 plus anti-cd28 in the absence ( ) or presence of HLI373 or DMSO. (g-i) IB analyses using GFP + thymocytes (g) or naïve CD4 + T cells (h) and IFN-γ ICS in stimulated GFP + naïve CD4 + T cells (n=5 mice/group; showing a representative plot) of Rag1 / mice adoptively transferred (for 6 wk) with Usp15 / bone marrow cells transduced with a GFP-expressing vector (EV) or the same vector encoding HA-tagged MDM2. (j) IB analysis using sorted (GFP + ) wild-type or Usp15 / naïve CD4 + T cells reconstituted, via bone marrow adoptive transfer, with a GFP-expressing vector (EV), USP15, or USP15C298A and stimulated as indicated. (k,l) qrt-pcr (k) and IB (l) analyses of wild-type naive CD4 + T cells stimulated with anti-cd3 plus anti-cd28 in the presence of DMSO or Nutlin-3 (n=3 mice/group). Data in summary graphs are mean ± s.e.m, and representative of at least three independent experiments. * P<0.05. Il2 mrna Ifng mrna IFN-γ

a NS IL-2 (pg/ml) Actin 100 50 CD4 + CD8 + 2 48 α-cd3/cd28 (h) Mdm2 mrna IFN-γ (pg/ml) 100 50 CD4 + CD8 + 2 48 1. 0. CD4 + CD8 + Usp15 mrna1. α-cd3/cd28 (h) Il2 mrna α-cd3 + α-cd28 (h) Lamin B 1 α-cd3/cd28 (h) WT KO 3 3 Ifng mrna 1 α-cd3/cd28 (h) NE CE Supplementary Figure 6. CD8 + T cells expressed lower levels of MDM2 and were not influenced by USP15 deficiency in cytokine production. (a) IB analysis of USP15 and MDM2 protein levels in CD4 + and CD8 + T cells. A nonspecific band is indicated as NS. (b) qrt-pcr analysis of Mdm2 and Usp15 mrna levels in CD4 + and CD8 + T cells (n=3 mice/group). (c) IB analysis of NFATc2 and loading controls in the nuclear (NE) and cytoplasmic (CE) extracts of wild-type (WT) or Usp15 / CD8 + T cells stimulated as indicated. (d,e) ELISA (d, n=3 mice/ group) and qrt-pcr (e, n=3 mice/group) analyses using wild-type and Usp15 / (KO) CD8 + T cells stimulated for the indicated time periods with anti-cd3 plus anti-cd28. Data are representative of three independent experiments. NS, P>0.05; **P<0.01.

a shrna EV EV USP1 p53 HSP60 f shrna p53 p21 Ctrl HCT11 Melanoma cell lines A37 shusp1 Trp53 +/+ C 1 PI shrna Trp53 / C 1 Ctrl 8.9 14.7 9.1 Annexin V Colorectal cancer cell lines g Apoptosis (%) 2 1 1 A37 HCT11 Trp53 +/+ * shrna C 1 shusp1 EV EV USP1 Apoptosis (%) 2 1 1 HCT11 Trp53 / C 1 shrna Apoptosis (%) 2 1 1 C 1 EV EV USP1 Ctrl shusp1 A37 B cells Thymus WT KO WT KO Supplementary Figure 7. USP15 was abundantly expressed in cancer cells and required for MDM2 expression and cancer cell survival. (a) IB analysis using whole-cell extracts of melanoma and colon cancer cell lines. (b) IB analysis of the indicated proteins in human primary dermal fibroblasts transduced with pgipz lentiviral vectors encoding either a control shrna (C) or two different USP15 shrnas. (c) IB analysis of the indicated proteins using wild-type (WT) or Usp15 / murine B cells and thymocytes. (d,e) Control shrna (Ctrl)-transduced or USP15 shrna (shusp15)-transduced A375 cells were reconstituted with either an empty vector (EV) or an RNAi-resistant USP15 expression vector. The cells were subject to IB analysis of the indicated proteins (d) or flow cytometric analysis of spontaneous apoptosis showing a representative plot (numbers in the figure panels indicate percentage of apoptotic cells) and a summary graph (e) (n=3 mice/group). (f) IB analysis of the indicated proteins using HCT116 Trp53 +/+ or HCT116 Trp53 / cells infected with control (C) or USP15 shrnas. (g) Apoptotis analyses of the HCT116 Trp53 +/+ and HCT116 Trp53 / cells (n=3 mice/group). Bar graphs are mean ± s.e.m. Data are representative of three independent experiments. *P<0.05; **P<0.01.

a shrna shrna TGF-β p-smad2 Smad2 MG132 C 1 DMSO C 1 A375 Cells C 1 + + + HCT116 Cells A375 Cells shrna Ctrl USP1 Ctrl USP1 CHX (min) 1 3612 1 3612 1 3612 1 3612 p53 HCT116 Cells C 1 + + + Pai1 mrna A375 Cells Ctrl shrna (1) shrna (2) UT TGF-β Smad7 mrna UT TGF-β Pai1 mrna 1 HCT116 Cells Ctrl shrna (1) shrna (2) UT TGF-β Smad7 mrna 1 UT TGF-β Supplementary Figure 8. USP15 regulated the stability of MDM2 but was dispensable for TGF-β signaling in A375 and HCT116 cells. (a) IB analysis of MDM2 in control (C) or USP15 knockdown (shrna 1 and shrna 2) A375 cells incubated for 4 h with10 µg/ml MG132 or the solvent control DMSO. (b) IB analysis of the indicated proteins in control (Ctrll) or USP15 knockdown (shrna 1) cells incubated with cycloheximide (50 µg/ml) for the indicated time periods. (c) A375 and HCT116 cells were stably infected with a non-silencing control shrna (C) or two different USP15 shrnas. The cells were serum-starved for 24 h and stimulated with TGF-β for 1h, and whole-cell lysates were subjected to IB analysis of the indicated phosphorylated (p-) and total proteins. (d,e) qrt-pcr analysis of Pai1 and Smad7 mrna in the indicated cells, either untreated (UT) or stimulated with TGF-β for 4h (n=3 mice/group; mean ± s.e.m.). Data are representative of three independent experiments.

a Tumor size (mm 2 ) 20 15 Ctrl shusp1 10 5 p53 11 13 1 17 19 21 Time after tumor injection (d) f 16 8 7 8 9 1 11 1 Time after tumor injection (d) Tumor size (mm 2 )24 B16 Ctrl B16 shusp15 shrna C sh g Number of CD4 + IFN-γ + T cells/g tumor (10 5 ) 8 Tumor size (mm 2 ) 20 15 10 5 HCT116 Trp53 / Ctrl shusp1 9 11 13 117 19 21 Time after tumor injection (d) h IFN-γ shrna C sh p53 p21 CD8 8.7 13.8 16 8 Tumor size (mm 2 )24 B16 Ctrl B16 shusp1 B16 Ctrl B16 shusp1 7 1 1 1 17 Time after tumor injection (d) IFN-γ + CD8 + T cells (%) 2 1 1 Supplementary Figure 9. USP15 regulated tumor growth and anti-tumor T-cell responses. (a) Growth curve of xenograft tumors in nude mice that were injected s.c. with HCT116 cells (1 10 7 cells per mouse) stably expressing a control (Ctrl) shrna or a USP15-specific shrna (shrna 1) (n=7 mice/group). (b) IB analysis of the indicated proteins using lysates the xenograft tumors collected on day 21 post injection. (c) Growth curve of xenograft tumors in nude mice injected s.c. with USP15-silenced HCT116 Trp53 / cells (5 10 6 cells per mouse) (n=5 mice/group). (d) IB analysis using control (Ctrl) or USP15-knockdown B16 tumor cells. (e,f) Growth curve of tumors in wild-type (WT) or Usp15 / (KO) mice injected s.c. with a low dose (5 10 5 cells per mouse) (e) or a high dose (5 10 6 cells per mouse) (f) of the indicated B16 cells (n=5 mice/group). (g,h) wild-type and Usp15 / mice were injected s.c. with B16 melanoma cells. After 15 days of challenge, tumors were removed for ICS and flow cytometry analyses of the number of IFN-γ-producing tumor-infiltrating CD4 + (g) and the frequency of IFN-γ-producing tumor-infiltrating CD8 + (h) T cells. Data are presented as a representative plot or a summary graph of multiple mice (n=5 mice/group). Summary graphs are mean ± s.e.m., and data are representative of three independent experiments. * P<0.05.

a Foxp3 CD 17.1 17. 13. 14. 20.1 19.8 Spleen dln TIL Foxp3 + CD4 + T cells in the spleen (%) Foxp3 + CD4 + T cells in the dln (%) Foxp3 + CD4 + T cells in the TIL (%) 2 2 1 1 1 1 8 28 2 2 1 1 NS NS NS Tumor size (mm 2 ) 24 16 8 No. of CD4 + T cells per spleen (10 5 ) WT (Rat IgG) KO (Rat IgG) KO (IFN-γ Ab) 7 9 11 13 1 Time after tumor injection (d) Supplementary Figure 10. USP15 deficiency promoted IFN-γ-dependent tumor suppression but did not influence Treg frequency. (a,b) Flow cytometry analysis of the frequency of Foxp3 + CD4 + T cells in the spleen, draining lymph node (dln), and tumor-infiltrating lymphocytes (TIL) of day 15 B16-challenged wild-type (WT) and Usp15 / mice. Data are presented as a representative plot (a) and a summary graph of multiple mice (n=10 mice/group) (b). (c) Tumor growth curves in wild-type or Usp15 / mice injected s.c. with B16 melanoma cells and administered i.p. with 0.5 mg of an anti-mouse IFN-γ neutralizing antibody or a rat IgG control every 3 days starting from day 1 of B16 challenge. (d) Flow cytometric analysis of splenic CD4 + T cells in Tcrb / Tcrd / mice reconstituted (for 16 days) with 5 10 6 wild-type or Usp15 / (KO) naïve CD4 + T cells in the presence of equal numbers of wild-type CD8 + T cells (n=5 mice/group). Summary graphs are mean ± s.e.m., and data are representative of three independent experiments. NS, P>0.05; * P<0.05. 3

Supplementary Table 1. Gene-specific primers used for RT-PCR Gene Forward primer Reverse primer mactb musp15(78-432) GGTACCACCATGTACCCAGG AGGGGACACCTGGTATCTAGT musp15(602-1191) CCGGCCTATACCAAGGACAG musp15(1892-2206) TACGTTGCTGTGAGGACCAG musp15(2504-2839) TCAAGAGATTCTCCTATAGTCGCT GAAAGGGTGTAAAACGCAGC CATGTTCCCGTTCTCACAGAG ATTCAGGTCCTCGTGCAGTC ATCGGATGTGACTGGTGTCG CTCGGTCAAGAGGGAAGAAGC

Supplementary Table 2. PCR primers used for generating USP15 truncation mutants Gene Primer husp15(fl) Forward primer Reverse primer husp15(aa114-981) Forward primer Reverse primer husp15(aa278-981) Forward primer Reverse primer husp15(aa470-981) Forward primer Reverse primer husp15(aa580-981) Forward primer Reverse primer husp15(aa1-941) Forward primer Reverse primer husp15(aa1-583) Forward primer Reverse primer CCCAAGCTTGGCATGGCGGAAGGCGGAGC GGGGTCGACTTAGTTAGTGTGCATACAGTTTTC GGGAAGCTTGCACGAAAGGTGGTTGAACAGG GGGGTCGACTTAGTTAGTGTGCATACAGTTTTC GGGAAGCTTGAACCTGGAAGAAACAATGAACAG GGGGTCGACTTAGTTAGTGTGCATACAGTTTTC GCCAAGCTTATGAAAAAAGAACGCACCTTGGAAG GGGGTCGACTTAGTTAGTGTGCATACAGTTTTC CCCAAGCTTTATACCCACCATACTGGTTCTTC GGGGTCGACTTAGTTAGTGTGCATACAGTTTTC CCCAAGCTTGGCATGGCGGAAGGCGGAGC GGGGTCGACTTAAAAGCCAGTTCCACTGAAAGTG CCCAAGCTTGGCATGGCGGAAGGCGGAGC GGGGTCGACTTAATGGTGGGTATAACTCGAGTGTC

Supplementary Table 3. Primers used for USP15 site-directed mutagenesis Gene Primer husp15c298a Forward primer Reverse primer husp15 RNAi-resistant mutant Forward primer Reverse primer CCTAAGTAACTTGGGAAATACGGCTTTTATGAACTCAGCTATTCAGTG CACTGAATAGCTGAGTTCATAAAAGCCGTATTTCCCAAGTTACTTAGG CAGACAGCACCATTCAAGATGCAGGCTTATATCAAGGACAGGTATTAG CTAATACCTGTCCTTGATATAAGCCTGCATCTTGAATGGTGCTGTCTG

Supplementary Table 4. Antibodies Antigen Label Clone Manufacture Use CD3 APC 145-2C11 ebioscience FC CD4 PacificBlue RM4-5 ebioscience FC CD8 PE-Cy7 53-6.7 ebioscience FC CD19 PE-Cy7 1D3 BD FC CD44 PE IM7 ebioscience FC CD62L FITC MEL-14 BD FC Foxp3 FITC FJK-16s ebioscience FC IL-2 PE JES6-5H4 ebioscience FC IL-17A PE ebio17b7 ebioscience FC IFN-γ APC XMG1.2 ebioscience FC Akt1 B-1 Santa Cruz WB β-actin AC-74 Sigma WB ERK K-23 Santa Cruz WB Flag M2 Sigma WB/IP Hsp60 H1 Santa Cruz WB HA 3F10 Roche WB Lamin B C20 Santa Cruz WB Lck 3A5 Santa Cruz WB K48 ubiquitin Apu2 Millipore WB MDM2 Ab-3 Millipore WB/IP MDM2 MD-219 Sigma WB/IP NFATc1 7A6 Santa Cruz WB NFATc2 4G6-G5 Santa Cruz WB/IP p21 M-19 Santa Cruz WB p53 FL-393 Santa Cruz WB p65 E495 Cell Signaling WB p-erk E-4 Santa Cruz WB p-akt (Ser473) D9E Cell Signaling WB p-src (Tyr416) 2101* Cell Signaling WB p-s6 (Ser235/236) D57.2.2E Cell Signaling WB p-smad2 (Ser245/250/255) 3104S* Cell Signaling WB p-smad3 (Ser423/425) C25A9 Cell Signaling WB p-zap70(tyr319)/syk(tyr352) 2701* Cell Signaling WB c-rel (N) sc-70* Santa Cruz WB S6 54D2 Cell Signaling WB Smad2 86F7 Cell Signaling WB Smad3 9513* Cell Signaling WB Ubiquitin P4D1 Santa Cruz WB USP15 2D5 Santa Cruz WB USP15 14354-1-AP* Proteintech WB/IP Zap70 1E7.2 Santa Cruz WB IFN-γ XMG1.2 ebioscience Neu IL-4 11B11 ebioscience Neu IFN-γ XMG1.2 BioXCell Neu Isotype control Ab HRPN BioXCell Neu FC, flow cytometry. WB, western blot. IP, immunoprecipitation. Neu, neutralization. *Catalogue number

Supplementary Table 5. Gene-specific primers used for qrt-pcr Gene Forward primer Reverse primer mactb mil- mifng mnfatc2 mmdm mp21 hactb hsmad7 hpai1 hpuma hmdm hp21 msmad7 mmyc mil mil17a mfoxp3 CGTGAAAAGATGACCCAGATCA CCTGAGCAGGATGGAGAATTACA CAGCAACAGCAAGGCGAAA AGCCGCACGCCTTCTACCA TCAGCTCCGTGGTTCCT CGCCGCGGTGTCAGAGTCTAGG CGAGGCCCAGAGCAAGAGAG ACCCGATGGATTTTCTCAAACC TGCTGGTGAATGCCCTCTACT AAGAGCAAATGAGCCAAACG TTAGAGCACCCTGTCACCAC TTAGCAGCGGAACAAGGAGT TCTCCCCCTCCTCCTTACTC AAACGACAAGAGGCGGACAC CGCCATGCACGGAGATG AGCGATGGTGGATGGCTCATGGTTAG GGCGAAAGTGGCAGAGAGGTAT CACAGCCTGGATGGCTACGT TCCAGA ACATGCCGCAGAG CTGGACCTGTGGGTTGTTGAC GATGTCCGTCTCGCCCTTCC GCTATCCTTCGCTTCCTCT CTGTGCGGAACAGGTCGGACA CGGTTGGCCTTAGGGTTCAG GCCAGATAATTCGTTCCCCCT CGGTCATTCCCAGGTTCTCTA GCAGAGCACAGGATTCACAG ATGTAATTCAGCATCCACCC GTGGAGAAACGGGAACCAG CAGGCTCCAGAAGAAGTTGG TGGTCACGCAGGGCAAAA CGAGCTCACTCTCTGTGGTGTT AGCTTTCCCTCCGCATTGACACAG AAGACCCCAGTGGCAGCAGAA

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