Reactivation of latent HIV-1 in central memory CD4+T cells through TLR-1/2 stimulation
© Novis et al.; licensee BioMed Central Ltd. 2013
Received: 18 March 2013
Accepted: 10 October 2013
Published: 24 October 2013
Toll-like receptors (TLRs) are crucial for recognition of pathogen-associated molecular patterns by cells of the innate immune system. TLRs are present and functional in CD4+ T cells. Memory CD4+ T cells, predominantly central memory cells (TCM), constitute the main reservoir of latent HIV-1. However, how TLR ligands affect the quiescence of latent HIV within central memory CD4+ T cells has not been studied.
We evaluated the ability of a broad panel of TLR agonists to reactivate latent HIV-1. The TLR-1/2 agonist Pam3CSK4 leads to viral reactivation of quiescent HIV in a model of latency based on cultured TCM and in resting CD4+ T cells isolated from aviremic patients. In addition, we investigated the signaling pathway associated with Pam3CSK4 involved in HIV-1 reactivation. We show that the transcription factors NFκB, NFAT and AP-1 cooperate to induce viral reactivation downstream of TLR-1/2 stimulation. Furthermore, increasing levels of cyclin T1 is not required for TLR-mediated viral reactivation, but induction of viral expression requires activated pTEFb. Finally, Pam3CSK4 reactivates latent HIV-1 in the absence of T cell activation or proliferation, in contrast to antigen stimulation.
Our findings suggest that the signaling through TLR-1/2 pathway via Pam3CSK4 or other reagents should be explored as an anti-latency strategy either alone or in combination with other anti-latency drugs.
The existence of latent reservoirs of HIV-infected cells constitutes the major impediment towards viral eradication. Latent infection is associated with undetectable levels of viral gene expression and appears to be non-cytopathic. However, upon reactivation, latent viruses enter an active mode of replication in which they are fully competent for spread and induction of disease [1–3]. The main latent reservoir is known to reside within the subset of CD4+ memory T cells [1–5]. The current thinking in the field is that a combination of agents that disrupt latency (“anti-latency” drugs), when given with continuous antiretroviral therapy (ART), may be an effective approach toward viral eradication [6–8].
Transient bursts or “blips” of HIV-1 replication occur even in patients whose virus is well suppressed by anti-retroviral therapy (ART) . The origin of viral “blips” is not known. Several factors can contribute to these viral blips, such as selection of drug resistant variants, antigen-driven target cell activation, vaccination, opportunistic infections or random variation of test measurements . Interestingly, several vaccination regimens [11–14] and pathogen infections [15–19] have been shown to transiently increase the levels of plasma RNA in HIV-1 infected patients even in the presence of ART. Therefore, it is tempting to speculate that exposure to microbial products may trigger reactivation of latent viruses and thus influence the size of the latent reservoir.
Pathogen infections are primarily sensed by the innate immune system through the interaction of conserved molecular structures named pathogen-associated molecular patterns (PAMPs) via host-encoded pattern recognition receptors (PRRs) [20, 21]. PRRs are germline-encoded receptors that recognize several classes of molecules typical of pathogens, such as proteins, lipids, carbohydrates and nucleic acids . Among PRRs, Toll-like receptors (TLRs) are the most widely studied. TLR-1, 2, 4, 5, 6 and 10 are present on the cell surface and recognize PAMPs derived from bacteria, fungi and protozoa. Whereas, TLR-3, 7, 8 and 9 are present in endosomal compartments and recognize mainly nucleic acids derived from bacteria and viruses [21, 22]. TLRs have been detected on cells of both the innate and adaptive immune system (such us dendritic cells, macrophages, granulocytes, T cells, B cells, NK cells and mast cells) as well as endothelial and epithelial cells .
However, little is known about whether and how TLR ligands affect the latent reservoir of HIV infection in central memory CD4+ T cells. We have analyzed the potential ability of TLR agonists to transactivate the HIV-1 LTR using a previously described method for the generation of latently infected central memory T cells (TCM) [24, 25]. We demonstrate that Pam3CSK4, a TLR-1/2 agonist, is able to reactivate latent HIV-1 in this in vitro model and in cells isolated from aviremic patients. This reactivation is NFκB, NFAT and AP-1-mediated and require pTEFb activity. This pathway differs from that initiated by T cell receptor engagement, which was shown to be mediated, in the same latency model, primarily by NFAT .
Importantly from the standpoint of therapeutic applications, Pam3CSK4-induced viral reactivation is achieved in the absence of T cell activation and proliferation. Therefore, the signaling pathway activated by Pam3CSK4 appears to be selective for latent, integrated viruses and represents an attractive therapeutic target that can be exploited in eradication strategies.
Pam3CSK4, a TLR-1/2 agonist, reactivates latent HIV-1 in cultured TCMcells
TLR-2 recognizes a variety of molecular patterns from viruses, bacteria, fungi and protozoa . The specificity of PAMP recognition by TLR-2 is somewhat broad because TLR-2 can form functional homodimers, as well as heterodimers with TLR-1, TLR-6, TLR-10 or Dectin-1 [30–33]. To test which TLR-2 homo or heterodimers are capable of reactivating latent viruses in cultured TCM cells, we incubated latently infected cells with ligands for TLR-2 that use different co-receptors. We tested the synthetic diacylated lipopeptide Pam2CSK4 and the N-terminal part of the diacylated lipoprotein derived from Mycoplasma salivarium, FSL-1, both of which have been shown to induce signaling through a TLR-2/6 complex , although some of these diacylated lipopeptides can also induce signaling in the absence of TLR-6 . We also tested zymosan, a β-glucan present in yeast cell wall, which uses the Dectin-1/TLR-2 complex as receptor . Finally, we tested lipoarabidomannan of Mycobacterium smegmatis (LAM-MS) and polysaccharide A of Bacteroides fragilis (PSA). These last two have been shown to induce signaling mainly through TLR-2 alone [36, 37]. As shown in Figure 1B, the TLR-1/2 agonist Pam3CSK4 was the only TLR-2 agonist able to induce reactivation of latent HIV-1 in cultured TCM. We confirmed the activities of all TLR-2 agonists to induce IL-8 production in THP-1 cells (Additional file 2: Figure S2B). Furthermore, Zymosan behaved as a strong inductor of HIV-1 expression in the cell line J-LAT 10.6 (Additional file 2: Figure S2A). Finally, Pam3CSK4, Pam2CSK4 and Zymosan were able to reactivate latent HIV-1 in the U1 cell line (Additional file 2: Figure S2C). These results suggest that signaling through TLR-2/TLR-1 complexes, but not other TLR-2-containing complexes, are able to reactivate latent HIV-1 in cultured TCM. Thus, we conclude that signals that use TLR-2 alone or TLR-2 in combination with TLR-6 or Dectin-1 are not sufficient to reactivate latent HIV-1 in cultured TCM.
We next decided to analyze the expression levels of TLR-1 and TLR-2 in cultured TCM and in ex vivo isolated memory CD4+ T cells from healthy donors. As shown in Figure 1C, we detected surface expression of both, TLR-1 and TLR-2, in cultured TCM. Also, both receptors were expressed comparably in the three main subsets of memory CD4+ T cells, namely TCM, TTM and TEM (Figure 1D).
To further confirm whether Pam3CSK4 was able to reactivate latent HIV-1 ex vivo, we performed two different assays using resting CD4+ T cells from aviremic patients. In the first one, cells were treated with IL-2, IL-2 plus Pam3CSK4 or IL-2 plus panobinostat, an HDAC inhibitor that has been shown to reactivate latent HIV-1 . Three days after treatment, intracellular HIV-1 unspliced mRNA was quantified by RT-PCR. As shown in Figure 1E, Pam3CSK4 increased the levels of US-RNA over IL-2 treatment control in 2 of the 7 patients compared with 5 of 7 for panobinostat. In one of the patients, neither Pam3CSK4 nor panobinostat was able to reactivate latent HIV over IL-2 control (Figure 1E, closed start symbol). In the second assay, cells from 4 aviremic patients were subjected to the quantitative viral outgrowth assay (Q-VOA) assay [39, 40]. In this case, exposure to Pam3CSK4 allowed recovery of replication competent virus from resting CD4+ T cells of 2 ART-suppressed patients, although, as is generally seen with HDAC inhibitors, the frequency of induction of HIV outgrowth was greater after cells were fully activated by mitogen (Figure 1F). In the fourth patient, the frequency of latent infection was very low (less than 1 infected cell in 5 million resting CD4+ T cells), and the activity of Pam3CSK4 could not be assessed.
Pam3CSK4 induces viral reactivation through the activation of NFκB, NFAT and AP-1 transcription factors
To further characterize the signaling pathway that leads to viral reactivation induced by Pam3CSK4 in cultured TCM, we used chemical inhibitors of known signaling pathways activated by TLRs. It is known that TLR-1/2 activates NFκB via MyD88 and the subsequent formation of a complex with IRAK1/IRAK4 and TRAF6. This complex leads to the activation of the IKK complex through the kinase TAK1 and the phosphorylation and degradation of IκBα leading to the activation and translocation to the nucleus of NFκB . To assess the role of NFκB in viral reactivation induced by Pam3CSK4, we incubated cells with BAY 11–7082, an inhibitor of IκBα phosphorylation. As shown in Figure 2B, BAY 11–7082 blocked an average of 60% of viral reactivation induced by Pam3CSK4. However, BAY 11–7082 had a minor inhibitory effect (less than 20% inhibition on average) on viral reactivation induced by αCD3/αCD28 (Figure 2B). This result is in agreement with our previous studies indicating an unexpected lack of requirement for NFκB toward viral reactivation after stimulation with αCD3/αCD28 . However, in a signaling pathway other than αCD3/αCD28, we showed that NFκB was active and required for reactivating latent viruses in a stimulus-dependent manner in cultured TCM.
MyD88 activation also leads to the activation of the MAP kinase cascade, in particular JNK and ERK-1/2, which leads to the activation of the transcription factor AP-1. Cooperation between these transcription factors, NFκB and AP-1, has been shown to transactivate the HIV-1 LTR in cells lines [42, 43]. To investigate the role of AP-1 in viral reactivation induced by Pam3CSK4, we incubated the cells with SP600125 or PD98059, known inhibitors of JNK and ERK-1/2 respectively [44, 45]. As shown in Figure 2B, both inhibitors significantly abrogated viral reactivation by Pam3CSK4.
We have previously shown that NFAT is required for viral reactivation mediated by αCD3/αCD28 in cultured TCM. In agreement with that finding, Cyclosporine A (CsA), a potent NFAT inhibitor, blocked viral reactivation induced with αCD3/αCD28 (Figure 2B). Interestingly, CsA was able to impair viral reactivation mediated by Pam3CSK4 by 55% on average. These data suggest NFAT is also required for viral reactivation downstream of Pam3CSK4.
We have previously shown that JNK and ERK inhibitors blocked viral reactivation mediated by Pam3CSK4 (Figure 2B). JNK and ERK are involved in the activation respectively of cJun and cFos, components of the transcription factor AP-1. As shown in Figure 3B, we detected nuclear translocation of cJun at 3 hours with either IL-2, Pam3CSK4 or αCD3/αCD28 stimulation (lanes 10, 12 and 14 compared with lane 8). The levels of nuclear translocation were slightly higher with Pam3CSK4 than with IL-2 alone (Figure 3B, compare lanes 10 and 12). Surprisingly, we were unable to detect nuclear translocation of cFos at any time with either IL-2 or Pam3CSK4 (Figure 3B, lanes 9 to 12). The inability to detect efficient nuclear translocation of cFos and cJun with Pam3CSK4 may be due to the low sensitivity of the assay. For this reason, we decided to analyze whether Pam3CSK4 could activate JNK and ERK. As shown in Figure 3C, treatment with Pam3CSK4 resulted in increased JNK and ERK phosphorylation (lane 5) above what was observed with IL-2 alone (lane 2). These results suggest than Pam3CSK4 can efficiently induce NFκB and NFAT translocation into the nucleus. Furthermore, Pam3CSK4 induces activation of the JNK and ERK pathways required for AP-1 activation.
Pam3CSK4 but not other TLR2 agonist triggers intracellular Ca2+influx
Taken together, these data suggest that Pam3CSK4 increases intracellular Ca2+ flux, which is consistent with NFAT nuclear translocation and its role on HIV-1 reactivation mediated by Pam3CSK4. Furthermore, the inability of Pam2CSK4 and LAM-MS to increase intracellular Ca2+ may explain their failure to transactivate the HIV-1 LTR (Figure 1B).
Pam3CSK4 reactivates HIV-1 in a tat-dependent manner but in the absence of upregulation of cyclin T1
Low levels of the pTEFb main components, cyclin T1 and pCDK9, have been proposed to limit the ability of the LTR to efficiently drive transcription in resting cells . We analyzed whether Pam3CSK4 induced an increase in the levels of cyclin T1 or in the phosphorylation levels of CDK9 in cultured TCM. As shown in Figure 5B, levels of cyclin T1 remained constant when cells were incubated with IL-2 alone or in the presence of Pam3CSK4 (lanes 1 to 7). In contrast, incubation with αCD3/αCD28 increased the total levels of cyclin T1 in culture TCM as previously described (lines 8 to 10) . We then analyzed the levels of CDK9 and pCDK9. It has been previously shown that CDK9 exists in two isoforms generated from two different promoters . Both isoforms can be found as part of pTEFb complexes . As shown in Figure 5B, cultured TCM express both isoforms and the total levels of each isoform of CDK9 (CDK955 and CDK942 as indicated in Figure 5B) did not change with any of the treatments. Levels of pCDK955 were drastically increased when cells were incubated with αCD3/αCD28 (Compare lanes 1 to 8 and 9). Pam3SCK4 was able to increase levels of pCDK955 at 12 h when compare with IL-2 treatment alone (Figure 5B, lines 2 and 5). These results indicate that Pam3CSK4 reactivates latent HIV in a pTEFb dependent manner but in the absence of cyclinT1 upregulation.
Pam3CSK4 reactivates latent HIV-1 in the absence of T cell activation and/or proliferation
Using this in vitro model, we have previously shown that IL-7 plus IL-2 can induce a low degree of viral reactivation in the presence of cellular proliferation . Cellular proliferation in the absence of viral reactivation has been proposed as a mechanism for maintenance of the latent reservoir [5, 54]. To address whether Pam3CSK4 was able to induce cellular proliferation, we stained cells with the cell proliferation dye CPD eFluor647. After staining, cells were incubated with IL-2 alone, Pam3CSK4 or αCD3/αCD28 and cellular proliferation and viral reactivation was measured 3 days later. As shown in Figure 6C, Pam3CSK4 induced viral reactivation in the absence of cellular proliferation when compared with our control treatment of IL-2 alone. However, reactivation through CD3 and CD28 led to massive cellular proliferation as well as viral reactivation from latency. These results indicate that Pam3CSK4 can reactivate latent HIV-1 in the absence of T cell activation or proliferation.
In this study, we have found that Pam3CSK4, a TLR-1/2 agonist, is able to reactivate HIV-1 from latency in primary cultured TCM cells. We have also tested the ability of Pam3CSK4 to reactivate latent HIV-1 in two ex vivo models. In this case, Pam3CSK4 is able to reactivate latent HIV-1 in a fraction of the patients. Several polymorphisms have been described to affect TLR-1/2 signaling [55–57]. It will be interesting to address whether these polymorphisms are associated with the ability of Pam3CSK4 to reactivate latent HIV-1 in memory CD4+ T cells.
Several PAMPs and their corresponding microorganisms have been shown to directly transactivate the HIV-1 LTR. Live mycobacteria as well as some of their components induce HIV-1 expression in human monocytes, lymphocytes, or cell lines in vitro[58–62]. This induction has been shown to be dependent on TLR-2 [62, 63]. Flagellin, a TLR-5 agonist, reactivates latent HIV-1 in the cell line J-Lat . Furthermore, the TLR-7/8 agonist, R-848, is able to reactivate latent HIV-1 from myeloid-monocytic cells lines . Finally, the TLR-9 agonist, CpG oligodeoxynucleotide, has been shown to reactivate latent HIV-1 in the cell line ACH-2 . In an independent study, performed while this work was in progress, Dr. Jonathan Karn and colleagues have found that TLR-5 agonist flagellin leads to viral reactivation from latency in microglial cells, and that the TLR-3 and TLR-9 agonist, poly (I:C) and ODN2006 respectively, weakly reactivate latent HIV-1 in a primary cell model of TH17 cells (manuscript in preparation).
TLR-2 recognizes a wide range of ligands because it functions in conjunction with other receptors . Thus, TLR-2 can form heterodimers with TLR-1 or TLR-6. TLR-1/2 complexes recognize triacylated lipopeptides whereas TLR-2/6 complexes recognize diacylated lipopeptides [34, 66]. In addition, TLR-2 has been shown to cooperate with TLR-10  and with the c-type lectin, Dectin-1 . We have shown that the triacylated lipopeptide Pam3CSK4 is the only TLR-2 agonist tested able to induce viral reactivation. Interestingly, Pam3CSK4 was able to induce an increase in intracellular calcium and subsequent activation of the transcription factor NFAT. We have shown that, in addition to the canonical pathway of NFκB and AP1 activation mediated by TLR-1/2, NFAT activation is also required for viral reactivation. Our result is in agreement with a published report showing that Pam3CSK4 stimulates release of Ca2+ from intracellular stores in lung fibroblast  and with several reports showing activation of NFAT after stimulation of bone marrow-derived macrophages with Pam3CSK4, zymosan and other TLR agonists [68, 69]. To our knowledge, this is the first time that it has been reported that Pam3CSK4 can activate NFAT in human primary CD4+ T cells.
We have previously demonstrated that NFAT but not NFκB plays a major role in viral reactivation through αCD3/αCD28 in cultured TCM (this report and ). On the other hand, stimulation with the TLR-1/2 agonist Pam3CSK4 leads to the activation of both NFκB and NFAT and both transcription factors are involved in viral reactivation mediated by Pam3CSK4. These results suggest that HIV-1 has evolved to use different transcription factors to increase viral transcription and that the ability of NFAT or NFκB to induce viral transcription is not determined by the viral LTR but by the stimulus.
It is well known that stimulation through CD3 and CD28 leads to large-scale T cell activation, release of cytokines and chemokines, massive T cell proliferation and ultimately leads to profound T cell depletion in humans [52, 53]. However, we show here that Pam3CSK4 is able to activate the HIV-1 promoter in a NFκB and NFAT-dependent manner; but it does so in the absence of overt signs of T cell activation, specifically, CD69, CD25 and T cell proliferation. We have identified several differences between the signaling pathways activated by αCD3/αCD28 and Pam3CSK4 that can account for the difference in T cell activation. First, αCD3/αCD28 induced a stronger nuclear translocation of the constitutive NFAT isoform NFATc2 and a better activation of the transcription factor AP-1. Both, AP-1 and NFAT form a quaternary complex during T-cell activation . Second, Pam3CSK4 is a more potent inductor of NFκB relative to αCD3/αCD28. Third, Pam3CSK4 does not increase the levels of cyclin T1 and induces low levels of pCDK9 whereas αCD3/αCD28 induce a strong increase of both, cyclin T1 and pCDK9. These results demonstrate that viral reactivation and cellular activation can be effectively decoupled. Also, these differences can have implications in the search for molecules that efficiently and safely reactivate latent HIV-1 virus in the absence of massive T cell activation. We hypothesized that those molecules that specifically activate NFκB, NFATc1, a weak AP-1 and do not upregulate cyclin T1 will be more desirable as anti-latency drugs than substances that induce a strong NFATc2, AP-1, cyclin T1 and pCDK9 responses.
Our results show that Pam3CSK4 has the potential to reactivate latent HIV-1 in TCM. These findings raise a series of important questions for further study: can Pam3CSK4 or other TLR agonists reactivate latent HIV in other primary cell models; are NFAT, NFκB and AP-1 recruited to the LTR following Pam3CSK4 signaling; why is the response to Pam3CSK4 heterogeneous in cells isolated from patients? As agents that can induce the expression of latent HIV without mediating global T cell activation are uncommon but highly valuable as potential drugs to attack the latent HIV reservoir, further study and testing of Pam3CSK4 and its signaling pathway is a high priority.
Although PAMPs are normally associated with infectious agents, their ability to enhance immune responses was documented in the context of cancer therapy a century ago, when William Coley used bacterial components named “Coley’s toxins” to treat cancer patients . Since then, several TLR agonists have been investigated for the use in treatment of cancer; viral or bacterial infections; allergy; asthma and autoimmunity (reviewed in ). In particular the triacylated lipopeptide outer surface protein A (OspA) of Borrelia burgdorferi, which is a TLR-1/2 agonist, has been previously clinically used as a vaccine against Lyme disease with minor side effects (reviewed in ). We suggest that triacylated lipopeptides and/or the TLR-1/2 signaling pathway can be targeted toward future development of anti-latency strategies, either alone or in combination with others anti-latency drugs.
The following reagents were obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID: Human rIL-2 from Dr. Maurice Gately, Hoffman-La Roche Inc. ; Monoclonal Antibody to HIV-1 p24 (AG3.0) from Dr. Jonathan Allan ; and Flavopiridol.
Generation of cultured TCMcells and their latent infection
Naïve CD4+ T cells were isolated via negative selection from peripheral blood mononuclear cells (PBMC) from healthy unidentified donors 18 years and older. Written informed consent was obtained from all donors. These studies are covered under the IRB #392 protocol approved by the University of Utah Institutional Review Board. Cultured TCM were generated and infected as previously described .
Stimulation of cells
2.5×105 cells were left untreated or stimulated for three days with the PRR agonists or beads coated with αCD3 and αCD28 (1 bead per cell, Dynal/Invitrogen, Carlsbad, CA). PRR agonists were obtained from Invivogen (San Diego, CA) and used at the concentration indicated: Pam3CSK4 (10 μg/ml), Pam2CSK4 (200 ng/ml), FSL-1 (10 μg/ml), Poly (I:C) HMW (10 μg/ml), LPS (10 μg/ml), flagellin (10 μg/ml), imiquimod (10 μg/ml), ssRNA40 (5 μg/ml), ODN2006 (5 μM), zymosan (200 μg/ml) and lipoarabinomannan from Mycobacterium smegmatis (LAM-MS) (10 μg/ml). TLR-2 agonist polysaccharide-A (PSA) was kindly provided by June Round (Pathology Department, University of Utah).
For inhibitors studies, cells were pre-incubated with the indicated inhibitors for 2 hours before stimulation. The inhibitors used were 1 μg/ml Cyclosporine-A (Sigma-Aldrich, Saint Louis, MO); 0.8 μM BAY 11-7082 and 50 μM PD98059 (Calbiochem, San Diego, CA); 25 μM SP600125 (A.G. Scientific Int., San Diego, CA); 50 nM and 100nM Flavopiridol (AIDS Research and Reference Reagent Program, Division of AIDS, NIAID).
Ex-vivoHIV-1 RNA reactivation assay
Frozen cells from 7 HIV-infected patients receiving HAART with plasma viral load <50 copies/ml for at least 6 months and CD4 count of >350 ul-1 were used for the ex-vivo HIV-1 RNA reactivation assay. A median of 50×106 frozen PBMCs were used to isolate CD4+ T cells using CD4+ T cell isolation kit (Milteny Biotec). CD4+ T cells were incubated in media containing 10 ug/ml Pam3CSK4 and 30 IU/ml IL-2, or 1uM Panobinostat and 30 U/ml IL-2. A background control well was set up with media supplemented with 30 U/ml IL-2. After 72 hours, total RNA was extracted and cDNA synthesized. Unspliced HIV-1 RNA was quantified by real-time PCR, using primers and probes previously described . Data were normalized to the expression of the housekeeping gene Actb (encoding b-actin). Results were plotted as a fold change induction of HIV-1 RNA expression between the test well and the background control well.
Quantitative viral outgrowth assay (Q-VOA)
Outgrowth assays were performed, as described previously . Briefly, PBMC were obtained by continuous-flow leukapheresis from HIV-infected volunteers receiving stable ART with plasma HIV-1 RNA less than 50 copies/ml and a CD4+ T cell count of more than 300 cells/ml. Resting CD4+ T cells were isolated by negative selection from PBMC and incubated in limiting dilutions with Pam3CSK4 or IL-2 for 24–48 hours or maximally stimulated with PHA-L, allogeneic irradiated PBMC from a sero-negative donor, and rIL-2. Cultures were fed twice with CD8-depleted PBMC, collected from a CCR5 high sero-negative donor. Supernatant was collected on days 15 and 19 and HIV p24 Gag antigen was measured by ELISA. Cultures that maintained an equivalent or greater level of p24 antigen on day 19 as on day 15 were scored as positive. A maximum likelihood method was used to calculate the infectious unit per million resting CD4+ T cells.
Flow cytometry analysis
Intracellular p24 Gag expression was analyzed as previously described .
Surface expression was determined using anti-human CD281-PE (TLR-1, clone GD2.F4, eBioscience, San Diego, CA), anti-human CD282-PE (TLR-2, clone TL2.1, eBioscience, San Diego, CA), anti-human CD25-FITC (Molecular Probes, Eugene, OR), anti-human CD69-FITC (Molecular Probes, Eugene, OR), anti-human CCR7-APC (R&D Systems, Minneapolis, MN) and anti-human CD27-FITC (Molecular Probes, Eugene, OR)
To analyze cell division with Cell Proliferation Dye eFluor 670 (eBioscience, San Diego, CA), cells were stained as indicated by the manufacturer.
Flow cytometry was performed with a BD FacsCanto II flow cytometer using the FACSDiva software (Becton Dickinson, Mountain View, CA). Data was analyzed with FlowJo (TreeStar Inc, Ashland, OR).
Intracellular calcium flux
Cells were loaded using Fluo-3 AM (Molecular Probes, Eugene, OR) following manufacturer’s protocol and analyzed by flow cytometry. Cells were left at room temperature in the dark, for 15 minutes. A 20 seconds baseline was recorded prior to addition of the stimulus. After addition of the stimulus cells were vortexed and analysis was performed during additional 150 seconds. 20 ng/ml of Ionomycin was used as a positive control.
To analyze phosphorylation, five million cultured TCM were lysed using a lysis buffer containing 50 mM Tris–HCl [pH 8], 150 mM NaCl, 1% NP-40, and 0.1% protease and phosphatase inhibitors (Roche Diagnostics, Indianapolis, IN) for 30 minutes at 4°C. Lysates were cleared by centrifugation at 12000 rpm for 20 min at 4C.
To analyze nuclear translocation, five million cultured TCM cells were washed in PBS and incubated with a cell lysis buffer containing 5 nM PIPES [pH8], 85 mM KCl, 0.5% NP-40 and 0.1% protease and phosphatase inhibitors for 30 min. After incubation, nuclei were pelleted by centrifugation at 5000 rpm during 20 min at 4°C. Supernatants were collected as cytoplasmic fractions. Nuclei were washed once with PBS containing 0.1% protease and phosphatase inhibitors and pelleted by centrifugation at 5000 rpm during 20 min at 4C. Nuclei were lysed with a buffer containing 50 mM Tris [pH 8.1], 10 nM EDTA, 1%SDS and 0.1% protease and phosphatase inhibitors and boiled for 10 min at 100°C. Nuclear extracts were cleared by centrifugation at 12000 rpm for 10 min at RT.
Proteins were separated on SDS-PAGE electrophoresis. Western blotting was performed according to the standard protocols. The following antibodies were used: p50, p65, NFATc1, NFATc2, cJun, cFos and cyclin-T1 (Santa Cruz Biotechnology, Santa Cruz, CA); total JNK, pJNK, total ERK, pERK, total CDK9 and pCDK9 (Cell Signaling, Danvers, MA); anti-β-actin antibody (Sigma-Aldrich, Saint Louis, MO); anti-α-tubulin antibody (Santa Cruz Biotechnology, Santa Cruz, CA) and anti-histone H3 (Biolegend, San Diego, CA).
Additional methods provided in Additional file 3.
We are grateful to Dr. Laura Martins, from the Department of Pathology, University of Utah, for careful reading of the manuscript. This work was supported by the National Institute of Health grants R21 AI106438-01 to A.B; R01 AI087508 to V.P; U19 AI096113 to D.M.M., E.V., and V.P.; and in part by the Bill and Melinda Gates Foundation Grand Challenges Explorations 7 (to A.B.).
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