INTRODUCTION
Type I interferons (IFNs) are potent antiviral cytokines that are primarily produced in response to the activation of pattern recognition receptors (
1,
2). Signaling through the ubiquitously expressed type I IFN receptor (IFNAR) leads to the robust and rapid increased expression of IFN-stimulated genes (ISGs) whose products affect cell growth, survival, differentiation, and the promotion of a core program of antiviral effector molecules (
3). The production of type I IFNs downstream of pattern recognition receptor activation and IFNAR signaling has largely been studied in myeloid cells, as part of the early innate immune response. However, type I IFN also modulates the phenotype and function of adaptive immune cells through the cell type–dependent induction of ISGs (
4). The effects of type I IFNs on T cells are highly context dependent; the phenotypic result is determined by additional signals and the differentiation status of the T cell receiving the signal (
5). These divergent outcomes suggest complex regulation of IFNAR signaling in CD4
+ T cells, but the specific mechanisms are unknown. Our study addresses this important gap in knowledge by describing a distinct role for tumor necrosis factor receptor (TNFR)–associated factor 3 (TRAF3) in promoting IFNAR signaling in CD4
+ T cells by preventing the recruitment of negative regulators.
Type I IFN initiates signaling by binding to the IFNAR2 subunit of the IFNAR complex, which in turn recruits the IFNAR1 subunit. Proximity of these IFNAR subunits then leads to transactivation of the Janus kinase (JAK) family members JAK1 and TYK2 (
6,
7). The JAK family members phosphorylate tyrosine residues in the cytoplasmic domains of IFNAR1 and IFNAR2, which enables the recruitment and activation of transcriptional activators called signal transducers and activators of transcription (STATs) (
8). In canonical IFNAR signaling, activated STAT1 and STAT2 heterodimerize and bind to IFN regulatory factor 9 (IRF9), forming a complex that translocates to the nucleus to activate the transcription of ISGs (
9). IFNAR signaling has potent downstream phenotypic effects; thus, it is tightly controlled by inducible and constitutively expressed proteins (
10). Among the constitutively expressed regulators are the protein tyrosine phosphatases PTP1B and PTPN2, which dephosphorylate TYK2 and JAK1, respectively (
11–
13). Inducible suppressor of cytokine signaling (SOCS) proteins decrease IFNAR signaling at later times; SOCS1 targets JAK1, TYK2, and STAT1 to inhibit antiviral responses induced by type I IFN (
14–
16).
TRAF3 is a widely expressed adaptor protein whose function varies by cell and receptor type. Lineage-specific deletion of TRAF3 revealed distinct roles for TRAF3 in Toll-like receptor, cytokine receptor, and antigen receptor signaling in both B and T lymphocytes (
17–
25). In conventional T cells, TRAF3 is necessary for the normal magnitude of signaling by the T cell antigen receptor (TCR) and TCR costimulatory receptors of the TNFR superfamily. Mice lacking TRAF3 in all mature T cells (T-
Traf3−/−) have normal T, B, and myeloid cell numbers but mount poor CD4
+ and CD8
+ T cell responses to infection by the intracellular bacterium
Listeria monocytogenes and cannot produce a T cell–dependent humoral response to immunization (
22). Many of the functional defects exhibited by TRAF3-deficient T cells originate with defective TCR signaling, which we described in T-
Traf3−/− mouse T cells and which was corroborated in human patients with one mutated
TRAF3 allele (
22,
26). A major role of TRAF3 in promoting TCR function is to interfere with negative regulators of early TCR signals. TRAF3 limits the localization of protein tyrosine phosphatase nonreceptor type 22 (PTPN22) and the negative regulatory kinase Csk to the TCR complex, thereby enhancing TCR signaling (
18). Furthermore, TRAF3 associates with the TCR signaling protein linker of activated T cells (LAT) and restrains Dok1, a negative regulator of LAT, through a mechanism involving PTP1B (
25).
Modulation of PTP localization and association with key signaling proteins are recurrent themes in the TRAF3-mediated regulation of cytokine and antigen receptors. For example, TRAF3 facilitates the association of the negative regulator PTPN22 with JAK1 at the interleukin-6 (IL-6) receptor in B cells to decrease signaling (
17). In thymic regulatory T (T
reg) cells, in contrast to its role in promoting TCR signaling, TRAF3 curbs IL-2 receptor (IL-2R) signaling by enabling the association of the negative regulator PTPN2 with JAK1 and JAK3 (
23). However, TRAF3 promotes IL-15 receptor signaling in invariant natural killer (iNK) T cells (
27). Thus, TRAF3 can both enhance and inhibit cytokine receptor signaling in a highly cell- and context-dependent manner.
The sequence of naïve T cell activation typically involves “signal 1” (from the TCR), “signal 2” (costimulation by CD28), and “signal 3” (signaling through cytokine receptors). In T cells, type I IFN can act as a signal 3 cytokine, promoting proliferation and the acquisition of effector functions (
28–
30). In the absence of the previous signals 1 and 2, type I IFN can exert pro-apoptotic and antiproliferative effects in CD8
+ T cells (
14,
31–
33). TRAF3 participates in signals 1 and 2 of T cell activation and cytokine signaling in other contexts, but its participation in signal 3, cytokine-mediated activation of T cells, is not well defined (
22,
24,
25,
34). The outcome of acute viral infections, including that by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), depends on the appropriate induction of and response to type I IFNs, particularly by adaptive immune cells (
35,
36). Here, we investigated the role of TRAF3 in the T cell–specific regulation of IFNAR signaling. We report that TRAF3-deficient CD4
+ T cells had reduced early IFNAR signaling events and that these early defects had long-lasting effects on the downstream consequences of IFNAR signaling. We provide evidence that the decrease in signaling in the absence of TRAF3 was due to aberrant recruitment of PTPN22, which can target JAK1, to the IFNAR signaling complex. Given the conflicting reports about the regulation of IFNAR signaling by PTPN22 in different cell types (
37,
38), our findings suggest that TRAF3 may control PTP access to cytokine receptors in a cell type–specific manner to prevent dysregulation.
DISCUSSION
Appropriate T cell responses are important for protection and recovery from infection, but inappropriate responses can be detrimental during autoimmune processes or in certain infectious contexts. Robust T cell activation depends on the receipt of three types of stimuli: signals through the TCR (signal 1), costimulatory receptors (signal 2), and cytokine receptors (signal 3). We previously reported that TRAF3 participates in the regulation of signals 1 and 2 (
22,
24,
25); here, we focused on the response to the important signal 3 cytokine type I IFN. We revealed a role for TRAF3 in blocking the negative regulation of IFNAR signaling in T cells by the tyrosine phosphatase PTPN22. PTPN22, also known as LYP in humans and PEP in mice, is a tyrosine phosphatase that regulates effector functions and signaling in many immune cell types (
41). PTPN22 variants with altered function can cause dysregulation of these effector functions, contributing to the pathogenesis of autoimmune diseases (
41,
42). The most common among these variants is R620W, which increases phosphatase activity but reduces the PTPN22-TRAF3 association (
37,
43). Our data from experiments with phosphatase-inactivating inhibitors show that PTPN22 phosphatase activity is required to restore IFNAR signaling to near WT levels in TRAF3-deficient cells.
TRAF3 promotes T cell–mediated immune responses through the inhibition of negative regulators, such as PTPN22, at the TCR as well. After TCR stimulation, TRAF3 sequesters PTPN22 in the cytoplasm, preventing it from dephosphorylating the early TCR signaling effector kinase Lck (
24). TRAF3 also sequesters the TCR-inhibitory kinase Csk in the cytoplasm during TCR signaling, preventing it from inactivating Lck. TRAF3 is recruited to the TCR complex through the adaptor protein LAT, and it also inhibits the negative regulation of LAT (
25). The cumulative effect of this segregation of negative regulators by TRAF3 is prolonged TCR signaling. The data shown here support a role for TRAF3 in preventing the inappropriate association of PTPN2 and PTPN22 with the IFNAR complex. TRAF3 additionally impedes signaling by the T cell costimulatory TNFR superfamily member GITR, through an incompletely understood mechanism that does not implicate phosphatase recruitment (
44). As discussed earlier, TRAF3 also limits T
reg cell differentiation by regulating the strength of IL-2R signaling on pre-T
reg cells (
23). Together, these findings indicate that TRAF3 overall enhances T cell activation, both by restraining or impeding the negative regulation of activating receptors in T cells and by restraining the functions of negative regulatory receptors, such as GITR, and the development of T
reg cells. These effects of TRAF3 in T cells stand in contrast to its negative regulation of activating receptors in B cells. For example, at IL-6R in B cells, TRAF3 enables PTPN22-mediated limitation of IL-6–induced JAK1 and STAT3 activation and thereby restrains plasma cell differentiation (
17). It will be interesting to determine whether TRAF3 impedes the access of PTPN22 or other phosphatases to additional receptors in T cells and to what extent its regulation of IFNAR involves the regulation of PTPN22 recruitment.
The main difference we observed between the primary mouse and transformed human TRAF3-deficient T cell phenotypes is the effect of TRAF3 on total STAT1 abundance. We showed here that a TRAF3-deficient human T cell lymphoma–derived cell line had reduced STAT1 abundance compared with that of WT cells, but this was not observed in mouse primary CD4
+ T cells. One possible explanation for this discrepancy is low-level STAT1 activation leading to a differential increase in STAT1 abundance between WT and TRAF3-deficient HuT28 cells. IFN-γ is made in small quantities by resting HuT28 cells, and IFN-γ activates STAT1, which amplifies the transcription of
STAT1. Such increases in STAT1 activity can last for days after IFN exposure (
40). Our data suggest that STAT1 activation after IFN-γ receptor signaling was decreased in TRAF3-deficient HuT28 cells (fig. S1); therefore, this basal activation may be sufficient to result in a difference in total STAT1 abundance. We would expect normal STAT1 activation to result in an increase in STAT1 abundance in TRAF3-sufficient HuT28 cells but not in TRAF3-deficient HuT28 cells. This hypothesis is particularly attractive because (i) we would not expect substantial or repeated exposure of T cells in a specific pathogen–free mouse to IFN-γ (thus, we would not expect there to be substantial differences in total STAT1 abundance between TRAF3-sufficient and TRAF3-deficient T cells) and (ii) our previous work established that compared with TRAF3-sufficient cells, TRAF3-deficient mouse CD4
+ T cells have enhanced activation of STAT1 in response to IFN-γ (
23). We would therefore expect any incidental exposures to IFN-γ to stimulate an increase in STAT1 abundance in the TRAF3-deficient mouse CD4
+ T cells compared with that in WT mouse CD4
+ T cells. We saw a trend toward slightly increased STAT1 abundance in the TRAF3-deficient mouse CD4
+ T cells (
Fig. 1F).
An intriguing question is what roles PTPN2 and PTPN22 play in IFNAR signaling in WT CD4
+ T cells. Published data are incomplete and conflicting as to how and where these phosphatases regulate IFNAR signaling, and it is unclear whether there are cell type–specific differences that may explain some of the discrepancies. Thymocytes from PTPN2-deficient mice exhibit enhanced STAT1 activation after stimulation with type I IFN, but the effect on JAK1 activation was only reported in response to IFN-γ stimulation (
11). PTPN22-deficient, bone marrow–derived macrophages have both enhanced and unchanged type I IFN–mediated STAT1 activation according to different reports (
37,
38). We showed here that neither PTPN2 nor PTPN22 was recruited to the IFNAR signaling complex within 15 min of the initiation of signaling, except in T cells lacking TRAF3. This suggests that neither phosphatase is a key early negative regulator of T cell IFNAR signaling in the presence of TRAF3. Inhibition of PTPN2 and PTPN22 also failed to enhance the extent of type I IFN–induced JAK1-STAT1 phosphorylation compared with that in unmanipulated WT T cells, further supporting the presence of TRAF3 as playing a key role in preventing early phosphatase activity. JAK1 is a well-established target of PTPN2 and is present at multiple receptor complexes that use JAK-STAT signaling. It seems likely that a key part of the function of TRAF3 is to prevent the inappropriate localization of PTPN2 to JAK1 in response to type I IFN signaling. The data from our PTPN2 inhibitor experiments did not provide evidence that PTPN2 inhibition detectably enhanced type I IFN–mediated STAT1 activation in T cells, but this apparent inconsistency with the limited published data may be due to additional pathway changes in PTPN2-deficient cells or to the different cell types used.
Last, it is important to consider the implications of our findings that TRAF3 modulates T cell IFNAR signaling in the context of an in vivo immune response. We are unable to obtain clearly interpretable data about this using currently available technologies because TRAF3 is an important regulator of TCR signaling, resulting in markedly defective in vivo T cell responses to infection and immunization in mice with a T cell–specific TRAF3 deficiency (
22). In addition, as discussed earlier, the inhibition of IL-2R signaling by TRAF3 results in an increased proportion of thymic-derived T
reg cells in these mice, further dampening their immune responses (
23). Discerning the effect of IFNAR signaling changes on the T cell response to an infection in vivo would be confounded by this suboptimal TCR signaling and downstream T cell activation as well as by the increased numbers of T
reg cells. On the basis of data showing the importance of type I IFN signals for T cells (
30,
45), we predict that a CD4
+ T cell selectively lacking TRAF3 involvement in IFNAR signaling would exhibit reduced proliferation and effector functions that are dependent on ISGs (for example, chemokine production). To conclude, this work highlights the importance of TRAF3 for signaling through IFNAR in CD4
+ T lymphocytes and provides insights into how PTPN2 and PTPN22 are prevented from premature interference with IFNAR signaling in T cells.
MATERIALS AND METHODS
Mice and cell lines
HuT78 cells transfected to stably express CD28 (HuT28.11, “Hut28”) were a gift from A. Weiss (University of California, San Francisco) (
46). PTPN22- and TRAF3-deficient HuT28 cells were generated with CRISPR-Cas9 technology as previously described (
24). TRAF3-deficient HuT28 cells were stably transfected with a plasmid encoding human
TRAF3 under the control of the Rous sarcoma virus promoter and containing a puromycin-resistance cassette. Single cells were plated after electroporation with plasmid, and clones that grew under puromycin selection (1.5 μg/ml, Gibco) were expanded for further analysis. HuT28 cells, knockout, and TRAF3-add back lines were cultured in complete medium [RPMI 1640 medium supplemented with penicillin (100 U/ml), streptomycin (100 U/ml), 2 mM
l-glutamine, 10 μM β-mercaptoethanol, and 10% fetal calf serum]. For experiments with cell lines, a biological replicate refers to an independent experiment performed on a different day from those of other replicates. Generation of B cell– and T cell–specific TRAF3 knockout mice has been previously described (
22,
47). Briefly, CD4-Cre mice were crossed to mice containing a floxed
Traf3 allele to delete
Traf3 in all mature T cells from the CD4
+CD8
+ developmental stage onward. In figures,
Traf3−/− denotes cells from CD4-Cre
+Traf3
fl/fl animals, and littermate control (referred to as WT for simplicity) denotes cells from CD4-Cre
−Traf3
fl/fl animals. The same breeding strategy with CD19-Cre mice instead of CD4-Cre mice was used to generate B cell–specific TRAF3 knockout mice. Mouse splenic and lymph node B or CD4
+ T cells were isolated by negative selection (STEMCELL Technologies, catalog nos. 19854 and 19852, respectively) according to the manufacturer’s instructions. Male and female mice were used, and mice were age- and sex-matched within each experiment. The Institutional Animal Care and Use Committee approved all procedures in this study under animal protocols 1062397 and 1091535.
Type I IFN stimulation, inhibitor treatment, and cell lysis
Primary mouse CD4
+ T cells and HuT28 cells were treated with human IFN-α hybrid (1000 U/ml; PBL Assay Science, 11200-2) in complete medium for the times indicated in the figures. Cells were lysed by vortexing in 1× radioimmunoprecipitation assay buffer (Cell Signaling Technology, #9806) containing 1 mM phenylmethylsulfonyl fluoride for whole-cell lysate analysis or immunoprecipitation (IP) lysis buffer [40 mM tris (pH 7.5), 0.5% Triton X-100, 100 mM NaCl, 1 mM MgCl
2, 1 mM CaCl
2, 2 mM Na
3VO
4, and EDTA-free cOmplete mini protease inhibitor cocktail (Roche)] for coimmunoprecipitation. Where indicated in the figures, 10 μM PTPN22 inhibitor LTV-1 (Calbiochem, catalog no. 540218), 20 μM PTPN22 inhibitor NC1 (Aobius, catalog no. AOB13736), 1 nM PTPN2 inhibitor SF-1670 (Tocris, catalog no. 5020), or an equal volume of dimethyl sulfoxide (DMSO) was included in the culture medium for 45 min (for LTV-1 and NC1) or 2 hours (for SF-1670) before and during stimulation of the cells with type I IFN (
37,
48).
Coimmunoprecipitations
Whole-cell lysates were prepared as described earlier and then precleared for 10 min with protein G Dynabeads (Invitrogen). Antibody recognizing one of the following targets was then added: JAK1 (MilliporeSigma, #05-1154, 1:1000 dilution), TRAF3 (Santa Cruz Biotechnology, #sc-1828, 1:1000, or Cell Signaling Technology, #4729, 1:100) or IFNAR1 (Abcam, #ab45172, 1:500). Lysates were incubated with the immunoprecipitating antibody for 2 hours at 4°C, and the antibody-bound targets were then captured with protein G Dynabeads for 20 min at 4°C. Dynabeads were washed three times with IP washing buffer [20 mM tris (pH 7.5), 1% Triton X-100, and 40 mM NaCl] and then resuspended in IP lysis buffer for Western blotting analysis.
Western blotting
Proteins were separated on bis-tris polyacrylamide gels and transferred to a polyvinylidene difluoride membrane with an XCell II blotting system (Invitrogen) according to the manufacturer’s recommendations. Membranes were blocked with 5% nonfat milk and incubated with primary antibody overnight at 4°C. Primary antibodies against the following proteins were used for Western blotting analysis: Cell Signaling Technology: JAK1 (#3344), pJAK1 Tyr1034/1035 (#3331), STAT1 (#9172), pSTAT1 Tyr701 (#9167), STAT2 (#4594), pSTAT2 Tyr690 (#88410), STAT3 (#4904), pSTAT3 Tyr705 (#9145), STAT5 (#25656), pSTAT5 Tyr694 (#4322), MX1 (#37849), PTPN22 (#14693), PTPN2 (#59835), TRAF3 (#4729), IRF1 (#8478), IRF9 (#28492), and SOCS1 (#68631); Santa Cruz Biotechnology: β-actin (#sc-47778), GAPDH (#sc-47724), and IRF7 (#sc-74472). After incubation with primary antibody, the membranes were washed and incubated with horseradish peroxidase (HRP)–conjugated goat anti-mouse immunoglobulin G (IgG) (Jackson ImmunoResearch Labs, #115-035-003) or HRP-conjugated goat anti-rabbit IgG (Jackson ImmunoResearch Labs, #111-035-144) for 2 hours at room temperature. Blots were developed with SuperSignal West Pico or Femto substrate (Thermo Fisher Scientific) and imaged with a low-light imaging system (LAS400, Fuji Medical Imaging). Densitometry of Western blots was performed with ImageStudio Lite software (LI-COR Biosciences). The density of a band for a protein of interest was divided by the density of the band for a loading control (actin or GAPDH) from the same sample to normalize protein abundance.
qPCR assays
RNA was extracted with the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. Complementary DNA (cDNA) was synthesized with SuperScript III First-Strand Synthesis SuperMix (Invitrogen). Quantitative polymerase chain reaction (qPCR) was performed with cDNA, primer pairs for target genes, and PerfeCta SYBR Green Fastmix (Quanta Biosciences). Reactions were run in QuantStudio 6 Flex (Applied Biosystems) with a standard cycling protocol (90°C for 2 min; 40 cycles of 95°C for 15 s, 60°C for 1 min). qPCR data were analyzed with the 2
−ΔΔCt method, where the ΔΔ cycle threshold (Ct) = [(
CT gene of interest −
CT housekeeping gene) stimulated − (
CT gene of interest −
CT housekeeping gene) unstimulated]. Where indicated on the
y axis, the ratio of the
CT of the gene of interest to the
CT of the housekeeping gene is graphed.
Actb was chosen as a housekeeping gene for mouse samples, and
HPRT (
49) was used for human samples. The following primers for qPCR were synthesized by Iowa DNA Technologies: mouse
Actb, 5′-CATTGCTGACAGGATGCAGAAGG-3′ (forward) and 5′-TGCTGGAAGGTGGACAGTGAGG-3′ (reverse); mouse
Cxcl10, 5′-ATCATCCCTGCGAGCCTATCCT-3′ (forward) and 5′-GACCTTTTTTGGCTAAACGCTTTC-3′ (reverse); mouse
Ifit1, 5′-TACAGGCTGGAGTGTGCTGAGA-3′ (forward) and 5′-CTCCACTTTCAGAGCCTTCGCA-3′ (reverse); mouse
Ifitm3, 5′-TTCTGCTGCCTGGGCTTCATAG-3′ (forward) and 5′-ACCAAGGTGCTGATGTTCAGGC-3′ (reverse); human
CXCL10, 5′-CGATTCTGATTTGCTGCCTTAT-3′ (forward) and 5′-GGCTTGCAGGAATAATTTCAAGT-3′ (reverse); human
MX1, 5′-GGCTGTTTACCAGACTCCGACA-3′ (forward) and 5′-CACAAAGCCTGGCAGCTCTCTA-3′ (reverse); and human
HPRT (
49), 5′-GGACTAATTATGGACAGGACTG-3′ (forward) and 5′-GCTCTTCAGTCTGATAAAATCTAC-3′ (reverse). The human
STAT1 (PPH00811C) primer mix was purchased from Qiagen.
Enzyme-linked immunosorbent assays
Human CXCL10 was detected in the culture medium of type I IFN–stimulated HuT28.11 cells with the Human CXCL10/IP-10 DuoSet ELISA (R&D Systems, catalog no. DY266-05). Mouse Cxcl10 was detected in the culture medium of type I IFN–stimulated CD4+ T cells with the Mouse Cxcl10/IP-10 DuoSet ELISA (R&D Systems, catalog no. DY466-05).
Statistical analysis
Data were graphed, and statistical tests were performed with GraphPad Prism software. Time courses were analyzed with mixed-effects analysis or two-way analysis of variance (ANOVA) with Sidak’s multiple comparisons post hoc test. Comparisons not involving multiple time points were analyzed with unpaired t tests.
Acknowledgments
We would like to thank A. Weiss (UCSF) for providing the HuT28.11 cell line. We are also grateful to J. Houtman and members of the Bishop laboratory for thoughtful input and technical assistance throughout the work on this project.
Funding: This work was funded by the NIH (grant R01 AI123107 to G.A.B., grant T32 AI007260 to E.L.H., and grant T32 HL007344 to E.L.H.), the Holden Comprehensive Cancer Center through its NIH grant P30CA086862 (to G.A.B.), and Senior Research Career Scientist award IK6 BX005392 from the Department of Veterans Affairs, Office of Research and Development (to G.A.B.).
Author contributions: Conceptualization: A.M.W., E.L.H., and G.A.B. Investigation: E.L.H. and A.M.W. Funding acquisition: G.A.B. Supervision: G.A.B. Writing of the original draft: E.L.H. Review and editing of the manuscript: E.L.H., A.M.W., and G.A.B.
Competing interests: The authors declare that they have no competing interests.
Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper or the Supplementary Materials.