- Research article
- Open Access
In silico prediction of Ebola Zaire GP1,2 immuno-dominant epitopes for the Balb/c mouse
© Dutta et al. 2015
- Received: 10 June 2015
- Accepted: 1 October 2015
- Published: 6 October 2015
Ebola is a Filovirus (FV) that induces a highly communicable and deadly hemorrhagic fever. Currently, there are no approved vaccines to treat FV infections. Protection from FV infection requires cell mediated and humoral immunity. Glycoprotein GP1,2 Fc Zaire, a recombinant FV human Fc fusion protein, has been shown to confer protection against mouse adapted Zaire Ebola virus. The present studies are focused upon identifying immunodominant epitopes using in silico methods and developing tetramers as a diagnostic reagent to detect cell mediated immune responses to GP1,2 Fc.
The GP1,2 Ebola Zaire sequence from the 1976 outbreak was analyzed by both BIMAS and SYFPEITHI algorithms to identify potential immuno-dominant epitopes. Several peptides were synthesized and screened in flow-based MHC stability studies. Three candidate peptides, P8, P9 and P10, were identified and, following immunization in Balb/c mice, all three peptides induced IFN-γ as detected by ELISpot and intracellular staining.
Significantly, P8, P9 and P10 generated robust cytotoxic T-cell responses (CTL) as determined by a flow cytometry-based Caspase assay. Antigen specific cells were also detected, using tetramers. Both P9 and P10 have sequence homology with highly conserved regions of several strains of FV.
In sum, three immunodominant sequences of the Ebola GP1,2 have been identified using in silico methods that may confer protection against mouse adapted Ebola Zaire. The development of tetramer reagents will provide unique insight into the potency and durability of medical countermeasure vaccines for known bioterrorism threat agents in preclinical models.
- Immunodominant epitopes
Filoviruses (FV) are single-stranded negative sense RNA viruses that infect humans and primates. FV quickly obtunds the immune system and dysregulates coagulation . The mortality rate can be up to 90 % and is species-dependent. FV are Category A bioterrorism agents, and there are currently no licensed vaccines or treatments. FV induce a myriad of cellular effects that quickly overwhelm the immune system, which results in compromised FV antigen processing and presentation capabilities , depleted T-cells and poor cytotoxic T-cell (CTL) response [3, 4] and abrogated protective antibody production [3, 5].
The Ebola GP1,2 glycoprotein is responsible for viral binding and entry. It is a trimer with a chalice-like form . The receptor binding region is inside the chalice and the exterior is highly glycosylated. The receptors binding domains and heptad repeats in the base are highly conserved sequences among the FV species. The ability to generate a cellular T-cell response contributes to surviving the disease. The role of T-cells in controlling Ebola and Marburg infections has been recognized [3, 4, 7]. In mice, CD8+ T-cell depletion and perforin knockouts studies using FV have shown the need for CTL to survive infection . However, the CTL responses to FV in non-human primates have not been well characterized given the technical challenges of working in a BSL-4 environment.
Several FV vaccine constructs have been demonstrated to be protective in mice, guinea-pigs and non-human primates (NHP). Irradiated Ebola virus encapsulated in liposomes containing lipid A elicited GP1,2 specific CTL response  and attenuated Venezuelan equine encephalitis virus replicons expressing GP1,2  showed protective responses in mice. An improved vaccination strategy using DNA plasmids expressing mixtures of different GP1,2 along with nucleoprotein (NP) and further boosting with recombinant adenovirus expressing GP1,2 proved effective in eliciting protection against live Ebola virus challenge in cynomolgus macaques . Vesicular stomatitis virus based vaccines encoding GP1,2 protected NHP from Bundibugyo Ebola virus . Respiratory tract immunization of NHP with a Newcastle disease virus-vectored vaccine showed protective response against Ebola virus challenge . Live attenuated rabies virus vaccine expressing GP1,2 has been proposed for its safe use for vaccination in humans and wildlife . Also, the recombinant protein, Ebola Zaire GP1,2 Fc, protected mice from lethal mouse adapted Ebola Zaire challenge .
Identifying immunodominant epitopes provides critical insight into the mechanism of protection to FV. Immunodominant peptides of EBOV GP1,2 [16–19] and Lassa GP1,2 and Ebola nucleoprotein have been determined [20, 21]. Importantly, MHC tetramer technology has simplified the study of antigen-specific CTLs to determine the functional sensitivities of T-cell populations . Tetramers are fluorochrome-conjugated peptide–major histocompatibility complex (pMHC) multimers that are used in the study of antigen-specific T-cells by enabling their visualization, enumeration, phenotypic characterization and have been extensively used to track T-cells ex-vivo following vaccination or during viral infection . As a result, tetramers can be used as surrogate markers of cell mediated immunity. On the other hand, B-cell mediated responses, especially antibodies specific to GP1,2 co-related with protection in NHPs and mice [24, 25]. The postexposure antibody treatments demonstrated to protect NHPs from filovirus infection . In sum, development of effective Ebola vaccine would require both protective CTLs as well as a robust antibody response to ensure survival to lethal Ebola challenge.
In the present study we identified immunodominant peptides of the GP1,2 from Ebola Zaire in Balb/C mice for the KD MHC using in silico algorithms. The objective was to generate tetramers that can be used to follow CTL. Peptide candidates were screened and three peptides stabilized the KD MHC: P8, EYLFEVDNL, amino acids (aa) 231–240; P9, LFLRATTEL, aa 571–579; and P10, LYDRLASTV, aa 161–169. Splenocytes from peptide immunized mice generated IFN-γ upon in vitro re-stimulation and induced apoptosis in peptide sensitized targets. Tetramers for all three peptides were generated that detected antigen specific T-cells following immunization. Significantly, two of the three epitopes are conserved within FV which suggests that tetramer reagents will be useful in following cell mediated responses to Zaire vaccine candidates such as GP1,2 recombinant proteins, GP1,2 expressing virus like particles, recombinant VSV, Adenoviruses and GP1,2 DNA vaccines.
In silico predictions of GP1,2 immuno-dominant epitopes
In silico predictions of Ebola Zaire GP1,2 epitopes
Ebola Zaire GP
NCBI Accession number Q05320.1
MHC stability studies using RMAS KD cells
ELISpot analysis of peptides
Intracellular staining for IFN-γ
In the current study, several hundred Ebola GP1,2 Zaire sequences were examined using in silico techniques. Nanomers that scored higher than 22 on SYFPEITHI or 150 on BIMAS are shown in Table 1. The SYFPEITHI algorithm provides a score based upon the pattern of amino acid sequences that preferentially bind to the MHC. The BIMAS score is based on binding affinities of single amino acids of the peptide, with each amino acid weighted the same, thereby providing an overall affinity to MHC. Following their synthesis, MHC stability was examined using KD expressing RMAS cells. The peptides were P8, EYLFEVDNL aa 231–240; P9, LFLRATTEL, aa 571–580 and P10, LYDRLASTV aa 161–170. P8 and P10 are from regions that are highly conserved across species Zaire Mayinga, Zaire Kikwit, Cote-d-Ivoire, Sudan Boniface, Sudan Gulu, Reston Virginia and Marburg Popp . P8 [18, 19] and P10 [17–19] have been previously reported as CTL epitopes in Zaire EBOV GP1,2; however we have performed immunological analysis of a immune-dominant P9 peptide, which has been submitted by Kent et al. to http://www.iedb.org/epId/91636. As shown in Fig. 1, all three stabilized expression of KD MHC, which is crucial for immunodominant epitopes.
ELISpot identifies cells secreting cytokines and has a limit of detection as low as 1:106 [27, 28]. The ELISpot also provides a convenient means of estimating the frequencies of IFN-γ producing cells . Using a rabies vaccine expressing Ebola virus glycoprotein, a strong ELISpot response was seen in mice using peptide pools of GP1,2 . In the study, the peptides P8, P9 and P10 induced IFN-γ release. However as shown in Fig. 2, in contrast to the KD stability studies, P10 elicited the greatest response followed by P9 and P8.
As shown in Fig. 3, all three peptides induced IFN-γ in CD8+ T-cells, implying that these peptides may provide significant protection against Ebola. Lassa GP1,2 peptide also elicited a IFN-γ signal in HLA-A2.1 transgenic mice . The ICS results were highly consistent with the ELISpot data.
Class I tetramers permit the rapid assessment of antigen specific CD8+ T-cells which is essential in monitoring immune responses to infections as well as vaccine development . Tetramers can often detect antigen specific T-cells that are of low abundance and undetectable by functional studies such as ELISpot and ICS [30–33]. Tetramers were developed for nucleoprotein epitopes of Ebola Zaire . In this study, peptides P8, P9 and P10 were used to generate Class I Tetramers (synthesized at NIAID). When mice were immunized with the peptides, a specific staining for each tetramer was observed as shown in Fig. 4. Furthermore, we sorted the cells based upon tetramer staining which greatly amplified the detection of epitope specific CD8+ T-cell population. This demonstrates the utility of the tetramer reagents that will greatly assist in the ongoing studies using GP1,2 from Ebola Zaire.
We have used a non-radioactive flow-based assay to detect apoptosis in peptide sensitized, DDAO labeled KD RMAS cells . Most importantly, the flow-based Caspase 3 generation assay is 10–50 times more sensitive than the chromium release assay . As shown in Fig. 5, we noted Caspase 3 in DDAO labeled targets at the low Effector to Target ratio of 1:1. The Caspase generation is a function of effector cell number and was reduced linearly for all three peptides as the number of effectors decreased. The Caspase-3 expression shown in Fig. 6 and the IFN-γ expression observed in ICS staining as seen in Fig. 4 were comparable and support each other. These results suggest that the peptides may play a significant role during vaccination and protection of Ebola infection. The results from the present study are consistent with earlier studies . In Rao et al., the peptides P1 and P2 were identified using classical CTL assays to Ebola Zaire. Both P1 and P2 were assessed using liposomes containing Ebola Zaire, though the E:T ratio used by Rao et al. was much higher than used in the present experiments. CTL generated by peptides have also been demonstrated for Ebola Zaire NP  and Lassa GP1,2 peptides  using a Chromium release assay.
In this paper, we have identified three immune-dominant KD epitopes of GP1,2 using in silico methods and evaluated their immunogenicity through in vitro and in vivo assays. Furthermore, we developed tetramers, which detect Ebola specific T-cells. These tetramer reagents will significantly contribute in evaluating cell-mediated responses to infection and also in determining the efficacy of prospective vaccine candidates in the field of Ebola vaccine research.
In silico epitope prediction
The amino acid sequence for the Ebola Zaire GP1,2 Mayinga 1976 strain, (NCBI accession number: AAB81004), was used in these experiments. The sequence, 676 aa long, was analyzed first using the BIMAS algorithm (http://www-bimas.cit.nih.gov/) followed by the SYFPEITHI algorithm (http://www.syfpeithi.de) for the KD MHC of Balb/c [Parker, 1994 13 /id]. The following Filoviruses were used for sequence alignment of GP1,2, and their NCBI accession numbers are indicated: Zaire Ebola virus (AAA96744.1); Sudan Ebola virus (AAP88031.1); Ebola Bundibugyo (YP_003815435); Tai Forest (YP_003815426.1); Reston Ebola virus (Q66799.1) and Lake Victoria Marburgvirus (P35254.1).
Peptides were synthesized by New England Peptide (Gardner, MA), using standard methodology. Peptides were >95 % pure. They were re-constituted in de-ionized water and kept frozen at −20 °C until use. All peptides were diluted in culture media: RPMI-1640 (Gibco, Green Island, NY) containing 10 % (v/v) heat-inactivated fetal bovine serum (FBS), 1 % (v/v) antibiotic-antimycotic solution (Gibco) and 2 mM glutamine (Gibco).
Balb/c female mice, 4–6 weeks of age, were obtained from the National Cancer Institute, Frederick, MD. Upon receipt, the mice were held for 7 days for acclimation in an Association for Assessment and Accreditation of Laboratory Animal Care International -approved facility with ad libitum access to food and water. All experiments were performed with the approval of the Food and Drug Administration, Center for Drug and Radiological Health Institutional Animal Care and Use Committee.
Mice were immunized intra-peritoneally with 100 μg of peptide and 140 μg of Hepatitis B virus helper peptide, TPPAYRPPNAPIL in 100 μl of Seppic Montanide (Fairfield, NJ). Initially, the peptides were diluted in sterile PBS and mixed with an equal volume of Seppic Montanide. Mice were boosted with equivalent dose on day 7. One week later, the mice were sacrificed with CO2 and their spleens were harvested. The spleens were placed in pre-warmed Hank’s Balanced Salt Solution (HBSS) and processed to single cell suspensions. The erythrocytes were lysed with Ammonium Chloride potassium lysing buffer (Gibco) and the cells were washed once and re-suspended in media. For GP1,2 immunization, 100 μg GP1,2 -Fc (Kindly, provided by Dr. Krishnamurthy Konduru, CBER/FDA) and 140 μg of Hepatitis B virus helper peptide, TPPAYRPPNAPIL in 100 μl of Seppic Montanide. Mice were boosted with equivalent dose on day 10. Ten days later, the mice were sacrificed with CO2 and their spleens were harvested. Spleens were then processed to single cell suspension as described above.
The frequency of interferon-γ (IFN-γ) producing cells was measured by ELISpot. Briefly, the Immobilon®-P polyvinylidene fluoride plates (Millipore, Billerica, MA) were treated with 15 μl 33 % ethanol (Pharmco, Shelbyville, KY) for 1 min, and washed 5 times with sterile H2O. These plates were coated with 0.1 M carbonate Buffer (Sigma) containing anti-mouse IFN-γ (Mabtech, Mariemont, OH), 15 μg/ml and refrigerated overnight at 4 °C. The plate was washed 3 times in sterile PBS. The plate was incubated with blocking buffer using 1 % Bovine Serum Albumin in HBSS for 2 h at 37 °C in culture. 105 splenocytes per well were plated within 1 h of harvest from peptide immunized mice and incubated with selected dilutions of peptide in six replicate wells. PMA and ionomycin treated splenocytes were used as a positive control in all experiments. Following an overnight incubation at 37 °C, the media was removed and the plate was incubated with 200 μl wash buffer (PBS containing 0.01 % Tween-20, Sigma) for 10 min at RT. Next, the plate was washed three times with wash buffer for 1 min at RT. The biotinylated detecting antibody (Mabtech) diluted 1:1000 in freshly made and filtered 1 % BSA/PBS was added and the plate was incubated for 2 h at RT. The plate was washed 3 times with wash buffer and twice with PBS. Next, streptavidin HRP (Jackson Immuno Research, West Grove, PA) diluted 1:500 in PBS containing 0.5 % FCS in PBS was added and the plate was incubated for 1 h at RT. Following washing, 50 μl TMB substrate (Mabtech) was added per well. Washing with deionized water stopped the reaction immediately. After drying, the plate was analyzed using an AID plate reader (Autoimmun Diagnostika, Strassberg, Germany).
Intracellular cytokine staining
Splenocytes from peptide immunized mice were incubated with 1 μM peptide for 1 h . Next, Brefeldin A (Sigma) was diluted 1:1000 and was added for overnight stimulation. The cells were harvested and washed with cold staining buffer. Staining buffer is composed of HBSS (Gibco) and 3 % FCS . The cells were blocked with anti-Fc (BD) for 30 min on ice, followed by a wash with FACS buffer. The cells were stained for CD8 FITC (BD) for 1 h on ice and then washed twice with FACS buffer. Next, the cells were fixed with BD Cytofix for 20 min at RT. The cells were either kept at 4 °C or processed for intracellular staining. To stain, the cells were re-suspended in permeabilization buffer (BD) and washed once with FACS buffer. The cells were then stained for 1 h with PE labeled anti-IFN-γ (BD). Following staining, the cells were washed twice with the permeabilization buffer and re-suspended in FACS buffer. The cells were analyzed by flow cytometry in a FACS Canto using DIVA software.
Cleaved active caspase-3 and flow cytometry based CTL assay
Splenocytes were cultured with 1 μM of the appropriate peptide for 5 days in culture media supplemented with 10 % T-stim (BD). The cultures were harvested and the cells were centrifuged on Lympholyte M cell separation media (Cedarlane Laboratories, Burlington, NC), washed once in media and adjusted to 106 cells/ml.
KD TAP deficient RMAS cells (a generous gift from Eric G. Pamer, Memorial Sloan Kettering Cancer Center), were maintained in RPMI-10. KD cells were incubated overnight with 1 μM of the appropriate peptide. KD cells were harvested, adjusted to 5 × 106 cells/ml and labeled with 0.6 μM 1,3-dichloro-7-hydroxy-9,9-dimethyl-2(9H)-Acridinone (DDAO; Invitrogen, Grand Island, NY) for 15 min at 37 °C. The reaction was stopped with the addition of complete media. The KD cells were washed once with RPMI-10 and adjusted to 106 cells/ml.
For the Caspase 3 Assay, DDAO labeled peptide pulsed KD cells, 105 in 100 μl of RPMI-10, known as “targets” (T) were added to a round bottom plate . Next, “effector” (E) cells, splenocytes, were added. The E: T ratio was varied from 1:1 to 0.1:1. The plate was spun at 200 rpm for 1 min and the cultures were incubated for 4 h at 37 °C. The cells were washed twice with FACS buffer. The cells were then permeabilized using the cytofix/cytoperm kit according to the manufacturer’s instruction (BD Biosciences) and stained with PE labeled rabbit-anti mouse cleaved Caspase 3 (CC3) at 1:100 dilution for 60 min (BD Biosciences). Cells were analyzed on a FACS Canto using FACS DIVA software.
Peptide stabilization of MHC
KD cells were washed twice in serum free AIM V media (Gibco), adjusted to 2 × 106 cells per ml and 80 μL was dispensed into each well of a round bottom plate. The peptides, 50 μM, were added to the plate . The plate was incubated for 18 h and then washed with FACS buffer. FITC labeled BB7.2 antibody (BD), diluted to 500 ng/ml, was added for 30 min. After washing the cells were analyzed via FACSCAN.
Tetramer staining and FACS ARIA sorting
Splenocytes, (10 × 106), from immunized animals were re-suspended in 200 μl sort buffer which contained 2 % FCS and 0.2 % Na azide (Sigma) in HBSS (FACS buffer). Fc receptors were blocked with the addition of anti-Fc (BD) for 20 min. Next, 2 μl of peptide specific PE-labeled tetramer (NIAID Tetramer facility, Atlanta, GA) was added and the cells were incubated for 1 h at 37 °C. After one wash with FACS buffer, the cells were stained with anti-CD3 FITC and CD8 PerCp. Following washing, the cells were fixed as described above and were sorted on a FACS ARIA with 106 events acquired.
All values are expressed as mean ± SD. Individual experiments were performed in at least triplicate (n ≥3). The software package Instat 2 (Graph Pad Prism, version 5; Graph Pad Software, San Diego, CA) was used for statistical analysis of data. Significant differences between groups were determined using student’s t-test or one-way analysis of variance (one-way ANOVA) followed by using either a Dunnett’s or Bonferroni’s post-hoc test to compare the significance of differences between means. A p-value <0.05 was considered significant.
This work was supported by CDRH/FDA - NIAID/NIH Interagency Agreement: 224-10-6010 (req. # 1075469), grants from the Medical countermeasures initiative (MCMi), intramural funding from the Food and Drug Administration, Biomedical Advanced Research and Development Authority (BARDA) and Defense Advanced Research Projects Agency (DARPA). This article reflects the views of the author and should not be construed to represent FDA’s views or policies.
The mention of commercial products, their sources, or their use in connection with material reported herein is not to be construed as either an actual or implied endorsement of such products by the Department of Health and Human Services. The findings and conclusions in this article have not been formally disseminated by the U.S. Food and Drug Administration and should not be construed to represent any Agency determination or policy.
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