A common epitope on gp41, IFN-alpha and IFN-beta induces protective activity

Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning

The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achieved using solid phase immuno-assays such as ELISA tests and western blots. Here, we describe a sero-diagnostic approach based on phage-display of epitope arrays we term "Domain-Scan". We harness Next-generation sequencing (NGS) to measure the serum binding to dozens of epitopes derived from HIV-1 and HCV simultaneously. The distinction of healthy individuals from those infected with either HIV-1 or HCV, is modeled as a machine-learning classification problem, in which each determinant ("domain") is considered as a feature, and its NGS read-out provides values that correspond to the level of determinant-specific antibodies in the sample. We show that following training of a machine-learning model on labeled examples, we can very accurately classify unlabeled samples and pinpoint the domains that contribute most to the classification. Our experimental/computational Domain-Scan approach is general and can be adapted to other pathogens as long as sufficient training samples are provided.

Inhibition of HIV-1 gp41 expression with hammerhead ribozymes

Despite great progress in the treatment of AIDS, HIV-1 remains one of the major concerns as a human pathogen. One of the therapeutic strategies against viral infections is the application of catalytic ribonucleic acids (ribozymes) that can significantly reduce expression of a target gene by site-specific hydrolysis of its mRNA. In the present paper, we report a study on the activity of several variants of hammerhead ribozymes targeting a conserved region within mRNA encoding HIV-1 envelope glycoprotein gp41. On the basis of the data from in vitro assays and gene silencing in the cultured cells, we propose a new hammerhead ribozyme targeting the gp41-encoding sequence that can be potentially used as a therapeutic agent in AIDS treatment. Moreover, we demonstrate that the hydrolytic activity of the ribozyme in the intracellular environment cannot be inferred solely from the results of in vitro experiments.

The gp41 epitope, QARVLAVERY, is highly conserved and a potent inducer of IgA that neutralizes HIV-1 and inhibits viral transcytosis

Mucosal surfaces are the predominant site of human immunodeficiency virus (HIV)-1 transmission. For prophylactic approaches to effectively prevent HIV infection and subsequent dissemination, the induction of mucosally relevant protective immunity will be critical. Here, we have characterized the antibody (Ab) response generated by a highly conserved gp41epitope, QARVLAVERY, in an optimized immunization model that elicits potent epitope-specific Abs in the serum, vaginal washes, and fecal secretions of immunized mice. Our results show that QARVLAVERY is indeed a potent inducer of IgA and importantly, QARVLAVERY-specific IgA was effective in neutralizing HIV and inhibiting viral transcytosis. Intriguingly, QARVLAVERY also generated an approximate 1:1 ratio of IgG:IgA in the serum of immunized mice, independent of the delivery regimen and produced early systemic IgA, even before IgG. In light of the significantly high IgA induction by QARVLAVERY and the functionality of epitope-specific Abs in the inhibition of HIV infection and transcytosis, QARVLAVERY is an attractive epitope to be considered in mucosal vaccination strategies against HIV.

Immunogenicity and specificity of the candidate multi-epitope-vaccines against HIV-1

The failure of some candidate HIV-1 vaccines may result from inducing very weak neutralization activity against representative primary viral isolates. Based on our hypothesis that epitope-vaccine may be a new strategy to induce high levels of neutralizing antibodies against HIV-1, we designed two candidate multi-epitope-vaccines, EP1 [C-G-(ELDKWA-GPGRAFY)2-K] and EP2 (CG-GPGRAFY-G-ELDKWA-G-RILAVERYLKD), containing three neutralizing epitopes (GPGRAFY, ELDKWA and RILAVERYLKD) on HIV-1 envelope protein, and expected them to induce epitope-specific antibodies of predefined epitope-specificity. The two peptides were conjugated to carrier protein bovine serum albumin (BSA) and used for immunization of rabbits. Proteins were purified from the rabbit sera induced by both candidate multi-epitope-vaccines (EP1-BSA and EP2-BSA) through affinity chromatography with epitope-peptide-conjugated sepharose-column, and identified as antibodies in silver-staining and immunoblotting. These antibodies were demonstrated to recognize three neutralizing epitopes on peptides and the recombinant gp41 in ELISA-assay and immunoblotting. These results indicated that both candidate multi-epitope-vaccines could induce high levels of antibodies of predefined epitope-specificity which recognized a few of neutralizing epitopes on peptides and protein, providing experimental evidence for the new strategy to develop an effective neutralizing-antibody-based multi-epitope-vaccine against HIV-1.

Characterization of interaction between C-domain on HIV-1 gp41 and the putative receptor protein p62

Based on the fact that the binding of HIV-1 gp41 to the putative cellular receptor protein p62 could be inhibited by the C-domain peptide of gp41, we wanted to confirm the interaction of the C-domain with p62 and to characterize the receptor-binding site on the C-domain. We attempted to isolate the putative receptor protein p62 from cell lysates of the human B cell line Raji by affinity chromatography using sepharose-columns which were conjugated with three different peptides of the C-domain respectively. A protein of 62 kDa was isolated by peptide (NP2)-sepharose-column, while none of the proteins was identified in eluates of the other two overlapped peptides of C-domain, indicating that HIV-1 gp41 by the region aa635-664 of C-domain binds to the putative receptor protein p62. Besides, CD spectroscopy analysis revealed that only a NP2 peptide could induce significant conformational change of P62. In addition, the interaction between P62 and three peptides of the C-domain was characterized by the surface plasma resonance (SPR) measurement. It was indicated that only the NP2 peptide significantly inhibited the interaction between rsgp41 and the putative receptor P62, confirming that the protein p62 may serve as a potential receptor for gp41 binding, and the peptide NP2 contains an integrate binding site for gp41 binding to p62.

HIV epitope-peptides in aluminum adjuvant induced high levels of epitope-specific antibodies

Some neutralizing epitopes on HIV-1 envelope proteins were shown to induce antibodies that could effectively inhibit the infection of different HIV-1 strains in vitro. But only very low levels of antibodies to these epitopes were determined in the HIV-1 infected individuals. In this study, the aluminum (alum) adjuvant to increase the immunogenicity of the neutralizing epitopes was used. Three epitope-peptides [C-(ELDKWAG)4, C-(RILAVERYLKD-G)2 and C-(GPGRAFY)2], which contain three epitopes (ELDKWA, RILAVERYLKD, GPGRAFY) from the HIV-1 Env proteins, were synthesized and conjugated to carrier protein keyhole limpet hemocyanin (KLH). The epitope-vaccines C-(ELDKWAG)4-KLH and C-(RILAVERYLKD-G)2-KLH in alum induced high levels of epitope-specific antibodies recognizing the epitopes from epitope-peptides C-(ELDKWAG)4 and C-(RILAVERYLKD-G)2, as well as the gp41 C-domain peptides P2 [C-TSLIHSLIEESQNQQEKNEQELLELDKWA (aa 646-674)] and P1 [LQARILAVERYLKDQQL (aa 583-599)] and the recombinant soluble gp41 (rsgp41) bearing both epitopes (antibody titer in rabbit sera was 1:12800-25,600 dilution). Immunoblotting analysis demonstrated that the antibodies in both antisera bound to rsgp41, indicating that both antibodies recognized the natural epitopes on rsgp41 protein. The epitope-vaccines C-(GPGRAFY)2-KLH induced moderate GPGRAFY epitope-specific antibody response with a titer of 1:6,400. In contrast, as it was demonstrated in previous studies, the immunization with rgp160 induced weak antibody response to these three epitopes (titer of 1:400-1600). This suggests that epitope-peptides conjugated to KLH when infected with alum significantly increases immunogenicity of gp41 neutralizing epitopes providing a hope for the development of an HIV-1 vaccine.

HIV-1 gp41 and type I interferon: sequence homology and biological as well as clinical implications

HIV-1 gp41-like human type I interferon (IFN) could inhibit lymphocyte proliferation and up-modulate MHC class I and II and ICAM-1 molecule expression. Sequence comparison indicates that a similar epitope RILAV-YLKD exists between N-domain of gp41 and two regions in IFN-alpha(aa29-35 and 113-129), IFN-beta (aa31-37 and 125-138) and IFN-omega (aa29-35 and 123-136), which was shown to form IFN-alpha/beta-receptor binding site. Weak sequence similarity was also found to exist in both regions on gp41 and type I IFN of murine and bovine. Experimental studies indicated that a common immunological epitope exists between gp41 and IFN-alpha and -beta. Antibodies against human IFN-alpha and -beta recognized the common immunological epitope and inhibited gp41-binding to the potential cellular receptor protein p45. Moreover, the polyclonal antibody to IFN-beta completely inhibited gp41-binding to human T, B cells and monocytic cells, while IFN-alpha could only inhibit this binding incompletely. It was interestingly observed that human IFN-beta after preincubating with cells could incompletely inhibit the binding of gp41 to human B cells and monocytic cells, and very weakly inhibit the binding to human T cells, indicating that the receptor for IFN-beta-binding may be involved in gp41 binding. This potential relationship may be based on the amino acid sequence homology in the receptor binding region between gp41 and IFN-beta. It was observed that the increased levels of antibodies against human IFN-alpha and -beta exist in HIV-1-infected individuals and are associated with the common epitope on gp41. Besides, several studies provided experimental evidence that the common immunological epitope could induce protective activity against HIV-1. The IFN-alpha-based vaccine has showed a significant reduction of disease progression in IFN-alpha-vaccine-treated HIV-infected patients. Recent experimental evidence indicates that gp41 and IFN-beta were involved in downregulation of CCR5 expression and induction of cell activation or signal transduction. Whether it may be performed by a similar mechanism is still to be investigated.

N- and C-domains of HIV-1 gp41: mutation, structure and functions

Recent studies demonstrated that the N- and C-domains of HIV-1 gp41 is involved in virus-mediated membrane fusion resulting in HIV-entry into the target cells. Up to now, viral mutation baffled many scientists to develop effective vaccines and drugs against HIV-1. To acquire more information of mutation of gp41 and to reveal the relationship of structure and function of the N- and C-domains, we compared and analyzed amino acid sequences of the gp41 ectodomain (aa 512-681) of 862 isolates from most HIV-1 clades (including A, B, C, D, E, F, G, H, I, J and O clades). A consensus sequence of the ectodomain with the highest frequency emerging on each position is constituted. The fusion domain and the N-domain belong to the most conserved regions in gp41, and most variable residues assemble partial to the C terminal of gp41. The hydrophobicity of each position is also calculated. The a and d positions in the N-domain for maintaining stabilization of the trimeric coiled coil interactions are highly conservative, and the e and g positions in the C-domain to retain the interaction show also highly conservative. The strange high conservation of the c residues may have an implication in the coiled coil structure. The highly conserved residues form the lining of the hydrophobic cavity and the deep cavity is an ideal target for small molecular inhibitors. On the C-terminal of the C-domain there is a highly conserved segment GIVQQQ. They are intimately involved in forming the three interfaces between neighboring helices. The function of the N- and C-domains, such as binding to the potential cellular receptor and inducing protective activities, are also discussed. These studies on the mutation, structure and functions of the N- and C-domains suggested that both domains become a new focus to develop effective vaccine and antiviral drugs in the new strategies.

Candidate multi-epitope vaccines in aluminium adjuvant induce high levels of antibodies with predefined multi-epitope specificity against HIV-1

Some neutralizing epitopes on HIV-1 envelope proteins were identified to induce antibodies which could effectively inhibit the infection of different strains in vitro. But only very low levels of these antibodies were determined in the HIV-1 infected individuals. To increase the levels of protective antibodies in vivo, we suggested multi-epitope vaccine as a new strategy to induce high level of neutralization antibodies with predefined multi-epitope specificity. A synthesized epitope peptide MP (CG-GPGRAFY-G-ELDKWA-G-RILAVERYLKD) containing three neutralizing epitopes (GPGRAFY, ELDKWA, RILAVERYLKD) was conjugated to carrier protein KLH, and then used for immunization in mouse together with aluminium adjuvant or Freund's adjuvant (FA). The candidate MP-KLH multi-epitope vaccine in aluminium adjuvant could induce antibody response very strongly to the epitope peptide C-(RILAVERYLKD-G)2 and the immunosuppressive peptide (P1) (LQARILAVERYLKDQQL) (antibody titer: 1:51200), strongly to the epitope peptide C-(ELDKWA-G)4 and the C-domain peptide (P2) (1:12800), and moderately to the epitope peptide C-(GPGRAFY)4 and the V3 loop peptide (1:1600). The immunoblotting analysis demonstrated that the antibodies in sera could recognize P1, P2, V3 loop peptides and rsgp41 (aa 539-684). These results are similar with that in the case of PI-BSA in FA, and suggest that the multi-epitope vaccine in aluminium could induce high levels of antibodies of predefined multi-epitope specificity, which provides experimental evidence for the new strategy to develop an effective neutralizing antibody-based multi-epitope vaccine against HIV-1.

Human interferon-beta inhibits binding of HIV-1 gp41 to lymphocyte and monocyte cells and binds the potential receptor protein P50 for HIV-1 gp41

Previous findings have indicated that HIV-1 gp41 like human type I interferon (IFN) could inhibit lymphocyte proliferation and up-modulate MHC class I, II and ICAM-1 molecule expression, and a common epitope exists between gp41 and type I interferon (IFN-alpha and -beta) in the receptor binding regions. To clarify the relationship between human type I interferon and HIV-1 gp41, we tried to inhibit recombinant soluble gp41-binding to human T, B and monocyte cell lines by human IFN-alpha, -beta and -gamma. It was interestingly observed that IFN-beta after preincubating with cells could inhibit the binding of rsgp41 to H9, Raji and U937 cells (T, B and monocyte cell lines), while this binding could not be inhibited by another type I interferon (IFN-alpha) and a type II interferon (IFN-gamma). It was further examined whether human IFN-alpha and -beta bind to the gp41 binding protein P50. In ELISA-assay, the human IFN-beta, but not IFN-alpha, could bind to P50 which was identified as a potential cellular receptor protein for gp41-binding. By the affinity capillary electrophoresis (ACE) analysis, formation of stable IFN-beta-P50 complex was observed. These results indicate that IFN-beta binds the potential receptor protein P50. Based on these experimental evidences and previous studies, it was presumed that the potential cellular receptor protein P50 may be the 51 kDa subunit of human IFN-alpha/beta receptor, which needs to be verified in the future.

Epitope-vaccine induces high levels of ELDKWA-epitope-specific neutralizing antibody

Based on the fact that mAb 2F5 recognizing ELDKWA-epitope on the C-domain of HIV-1 gp41 has significant neutralization potency against 90% of the investigated viruses of African, Asian, American and European strains, we attempted to characterise immunogenicity of the ELDKWA-epitope on an epitope-vaccine, and to produce ELDKWA-epitope-specific monoclonal antibodies (mAb) induced by the epitope-vaccine. The C-domain peptide (P2) and the ELDKWA-tetramer peptide [C-(ELDKWAG)4] were conjugated with BSA or P24-EC (GPKEPFRDYVDRFYK, a peptide of HIV-1 gag-protein P24, proved to be a good carrier peptide to induce an immune response to the hapten on the conjugates[18])by different methods. After the vaccination course, two P2-BSA peptide-vaccines both induced a strong antibody response against the P2-peptide by about 1:12800-25600 dilution, and a weak antibody response against the ELDKWA-epitope (1:1600-3200). The P2-P24EC and P2 (conjugated with itself) peptide-vaccines could also induce a weak antibody response against the ELDKWA-epitope (1:1600-3200), while an rgp160 subunit vaccine induced a very weak antibody response (1:400). Interestingly, the ELDKWA-tetramer epitope-vaccine [C-(ELDKWAG)4-BSA] could induce a strong antibody response against the ELDKWA-epitope (1:12800-25600), i.e. It increased the level of ELDKWA-antibody eight-fold, clearly better than the P2 peptide-vaccine, and much better than the rgp160 subunit vaccine, which indicates that the immunogenicities of the ELDKWA-epitope on the ELDKWA-tetramer peptide, the C-domain peptide and rgp160 are very different. These results suggest that the ELDKWA-epitope-vaccine may be a new strategy for inducing high levels of epitope-specific neutralizing antibodies against HIV-1. Using hybridoma-technique, a mouse monoclonal antibody recognizing the ELDKWA-epitope on ELDKWA-peptide and C-domain peptide was produced by immunization with the C-(ELDKWAG)4-BSA epitope-vaccine, which indicates a new way to produce an epitope-specific mAb, namely immunization with epitope-vaccine instead of a natural or recombinant protein immunogen.

Epitope-vaccines: a new strategy to induce high levels of neutralizing antibodies against HIV-1

Based on the experimental evidence that gp120 subunit vaccine did not protect individuals from HIV-1 infection, we suggested that epitope-vaccines of HIV-1 gp41 may be a new strategy to induce high levels of neutralizing antibodies against HIV-1, and characterised immunogenicity of epitope-vaccines. Two epitopes, RILAVERYLKD-epitope (aa586-596) on the N-domain and ELDKWA-epitope (aa669-674) on the C-domain of gp41, were demonstrated by us and others to induce protective activity. After vaccination course, the RILAVERYLKD-dimer epitope-vaccine [C(RILAVERYLKDG)2-BSA] induced strong epitope-specific antibody response by about 1:25,600 dilution, and the ELDKWA-tetramer epitope-vaccine [C-(ELDKWAG)4-BSA] could yet induce strong antibody response to ELDKWA-epitope by 1:12,800-25,600 dilution of antisera in mice, while rgp41 subunit vaccine induced very weak antibody response to both epitopes (1:400). In rabbit experiments, the titres of ELDKWA-epitope-specific antibody induced by ELDKWA-epitope-vaccine [C-(ELDKWAG)4-BSA] reached to 1:6,400, while rgp41 subunit vaccine induced very weak antibody response to this epitope and to P1 and P2 peptides (1:400). Moreover, the ELDKWA-epitope-specific antibodies in mice and rabbit antisera induced by epitope-vaccine could very strongly interact with P2 peptide sequence-corresponding to the C-domain of gp41 (dilution by 1:25,600), and the RILAVERYLKD-epitope-specific antibodies in mice antisera induced by epitope-vaccine could also very strongly interact with P1 peptide sequence-corresponding to the N-domain of gp41 (dilution by 1:102,400). All these results provided experimental evidence that epitope-vaccine may be a new general strategy to induce high levels of neutralizing antibodies against HIV-1 or other viruses.