AIDS Vaccine Design Immunogenicity Efficacy
Malherbe, D. C., J. Mendy, L. Vang, P. T. Barnette, J. Reed, S. K. Lakhashe, J. Owuor, J. S. Gach, A. W. Legasse, M. K. Axthelm, C. C. LaBranche, D. Montefiori, D. N. Forthal, B. Park, J. M. Wilson, J. H. McLinden, J. Xiang, J. T. Stapleton, J. B. Sacha, B. F. Haynes, H. X. Liao, R. M. Ruprecht, J. Smith, M. Gurwith, N. L. Haigwood and J. Alexander (2017). “Combination Adenovirus and Protein Vaccines Prevent Infection or Reduce Viral Burden after Heterologous Clade C SHIV Mucosal Challenge.” J Virol.
HIV vaccine development is focused on designing immunogens and delivery methods that elicit protective immunity. We evaluated a combination of Ad vectors expressing HIV 1086.C (Clade C) Envelope glycoprotein, SIV Gag p55, and human pegivirus GBV-C E2 glycoprotein. We compared replicating simian (SAd7) with non-replicating human (Ad4) adenovirus-vectored vaccines paired with recombinant proteins in a novel prime-boost regimen in rhesus macaques, with the goal of eliciting protective immunity against SHIV challenge. In both vaccine groups plasma and buccal Env-specific IgG, Tier 1 heterologous neutralizing antibodies, and ADCVI were readily generated. High Env-specific T cell responses elicited in all vaccinees were significantly greater than responses targeting Gag. Following three intrarectal exposures to heterologous Tier 1 Clade C SHIV, all 10 sham vaccinated controls were infected, while 4/10 SAd7 and 3/10 Ad4 vaccinated macaques remained uninfected or maintained tightly controlled plasma viremia. Time to infection was significantly delayed in SAd7-vaccinated macaques compared to the controls. Cell-associated and plasma virus levels were significantly lower in each group of vaccinated macaques compared with controls; the lowest plasma viral burden was found in those vaccinated with the SAd7 vectors, suggesting superior immunity conferred by the replicating simian vectors. Furthermore, higher V1V2-specific binding antibody titers correlated with viral control in the SAd7 vaccine group. Thus recombinant Ad plus protein vaccines generated humoral and cellular immunity that was effective in either protecting from SHIV acquisition or significantly reducing viremia in animals that became infected, consequently supporting additional development of replicating Ad vectors as HIV vaccines. IMPORTANCE There is a well-acknowledged need for an effective AIDS vaccine that protects against HIV infection and limits in vivo viral replication and associated pathogenesis. Although replicating virus vectors have been advanced as HIV-vaccine platforms, there have not been any direct comparisons of the replicating to the non-replicating format. The current study directly compared the replicating SAd7 to non-replicating Ad4 vectors in macaques and demonstrated that in the SAd7 vaccine group, time to infection was significantly delayed compared to the control group, and V1V2 Env-specific binding antibodies correlated with viral outcomes. Viral control was significantly enhanced in vaccinated macaques compared to controls, and in infected SAd7-vaccinated macaques compared to Ad4-vaccinated macaques, suggesting that this vector may have conferred more effective immunity. Because blocking infection is so difficult with current vaccines, development of a vaccine that can limit viremia if infection occurs would be valuable. These data support further development of replicating adenovirus vectors.
AIDS Vaccine Envelope Design
Cai, H., J. Orwenyo, J. P. Giddens, Q. Yang, R. Zhang, C. C. LaBranche, D. C. Montefiori and L. X. Wang (2017). “Synthetic Three-Component HIV-1 V3 Glycopeptide Immunogens Induce Glycan-Dependent Antibody Responses.” Cell Chem Biol.
Eliciting broadly neutralizing antibody (bNAb) responses against HIV-1 is a major goal for a prophylactic HIV-1 vaccine. One approach is to design immunogens based on known broadly neutralizing epitopes. Here we report the design and synthesis of an HIV-1 glycopeptide immunogen derived from the V3 domain. We performed glycopeptide epitope mapping to determine the minimal glycopeptide sequence as the epitope of V3-glycan-specific bNAbs PGT128 and 10-1074. We further constructed a self-adjuvant three-component immunogen that consists of a 33-mer V3 glycopeptide epitope, a universal T helper epitope P30, and a lipopeptide (Pam3CSK4) that serves as a ligand of Toll-like receptor 2. Rabbit immunization revealed that the synthetic self-adjuvant glycopeptide could elicit substantial glycan-dependent antibodies that exhibited broader recognition of HIV-1 gp120s than the non-glycosylated V3 peptide. These results suggest that the self-adjuvant synthetic glycopeptides can serve as an important component to elicit glycan-specific antibodies in HIV vaccine design.
Sullivan, J. T., C. Sulli, A. Nilo, A. Yasmeen, G. Ozorowski, R. W. Sanders, A. B. Ward, P. J. Klasse, J. P. Moore and B. J. Doranz (2017). “High-Throughput Protein Engineering Improves the Antigenicity and Stability of Soluble HIV-1 Envelope Glycoprotein SOSIP Trimers.” J Virol 91(22).
Soluble envelope glycoprotein (Env) trimers (SOSIP.664 gp140) are attractive HIV-1 vaccine candidates, with structures that mimic the native membrane-bound Env spike (gp160). Since engineering trimers can be limited by the difficulty of rationally predicting beneficial mutations, here we used a more comprehensive mutagenesis approach with the goal of identifying trimer variants with improved antigenic and stability properties. We created 341 cysteine pairs at predicted points of stabilization throughout gp140, 149 proline residue substitutions at every residue of the gp41 ectodomain, and 362 space-filling residue substitutions at every hydrophobic and aromatic residue in gp140. The parental protein target, the clade B strain B41 SOSIP.664 gp140, does not bind the broadly neutralizing antibody PGT151 and so was used here to identify improved variants that also provide insight into the structural basis for Env antigenicity. Each of the 852 mutants was expressed in human cells and screened for antigenicity using four different monoclonal antibodies (MAbs), including PGT151. We identified 29 trimer variants with antigenic improvements derived from each of the three mutagenesis strategies. We selected four variants (Q203F, T538F, I548F, and M629P) for more comprehensive biochemical, structural, and antigenicity analyses. The T538F substitution had the most beneficial effect overall, including restoration of the PGT151 epitope. The improved B41 SOSIP.664 trimer variants identified here may be useful for vaccine and structural studies. IMPORTANCE Soluble Env trimers have become attractive HIV-1 vaccine candidates, but the prototype designs are capable of further improvement through protein engineering. Using a high-throughput screening technology (shotgun mutagenesis) to create and evaluate 852 variants, we were able to identify sequence changes that were beneficial to the antigenicity and stability of soluble trimers based on the clade B B41 env gene. The strategies described here may be useful for identifying a wider range of antigenically and structurally improved soluble trimers based on multiple genotypes for use in programs intended to create a broadly protective HIV-1 vaccine.
Emerging Infectious Diseases
Kupferschmidt, K. (2017). “Genomes rewrite cholera’s global story.” Science 358(6364): 706-707.
Weill, F.-X., D. Domman, E. Njamkepo, C. Tarr, J. Rauzier, N. Fawal, K. H. Keddy, H. Salje, S. Moore, A. K. Mukhopadhyay, R. Bercion, F. J. Luquero, A. Ngandjio, M. Dosso, E. Monakhova, B. Garin, C. Bouchier, C. Pazzani, A. Mutreja, R. Grunow, F. Sidikou, L. Bonte, S. Breurec, M. Damian, B.-M. Njanpop-Lafourcade, G. Sapriel, A.-L. Page, M. Hamze, M. Henkens, G. Chowdhury, M. Mengel, J.-L. Koeck, J.-M. Fournier, G. Dougan, P. A. D. Grimont, J. Parkhill, K. E. Holt, R. Piarroux, T. Ramamurthy, M.-L. Quilici and N. R. Thomson (2017). “Genomic history of the seventh pandemic of cholera in Africa.” Science 358(6364): 785-789.
The cholera pathogen, Vibrio cholerae, is considered to be ubiquitous in water systems, making the design of eradication measures apparently fruitless. Nevertheless, local and global Vibrio populations remain distinct. Now, Weill et al. and Domman et al. show that a surprising diversity between continents has been established. Latin America and Africa bear different variants of cholera toxin with different transmission dynamics and ecological niches. The data are not consistent with the establishment of long-term reservoirs of pandemic cholera or with a relationship to climate events. Science, this issue p. 785, p. 789The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa.
Domman, D., M.-L. Quilici, M. J. Dorman, E. Njamkepo, A. Mutreja, A. E. Mather, G. Delgado, R. Morales-Espinosa, P. A. D. Grimont, M. L. Lizárraga-Partida, C. Bouchier, D. M. Aanensen, P. Kuri-Morales, C. L. Tarr, G. Dougan, J. Parkhill, J. Campos, A. Cravioto, F.-X. Weill and N. R. Thomson (2017). “Integrated view of Vibrio cholerae in the Americas.” Science 358(6364): 789-793.
The cholera pathogen, Vibrio cholerae, is considered to be ubiquitous in water systems, making the design of eradication measures apparently fruitless. Nevertheless, local and global Vibrio populations remain distinct. Now, Weill et al. and Domman et al. show that a surprising diversity between continents has been established. Latin America and Africa bear different variants of cholera toxin with different transmission dynamics and ecological niches. The data are not consistent with the establishment of long-term reservoirs of pandemic cholera or with a relationship to climate events. Science, this issue p. 785, p. 789Latin America has experienced two of the largest cholera epidemics in modern history; one in 1991 and the other in 2010. However, confusion still surrounds the relationships between globally circulating pandemic Vibrio cholerae clones and local bacterial populations. We used whole-genome sequencing to characterize cholera across the Americas over a 40-year time span. We found that both epidemics were the result of intercontinental introductions of seventh pandemic El Tor V. cholerae and that at least seven lineages local to the Americas are associated with disease that differs epidemiologically from epidemic cholera. Our results consolidate historical accounts of pandemic cholera with data to show the importance of local lineages, presenting an integrated view of cholera that is important to the design of future disease control strategies.
Fernandez, E., W. Dejnirattisai, B. Cao, S. M. Scheaffer, P. Supasa, W. Wongwiwat, P. Esakky, A. Drury, J. Mongkolsapaya, K. H. Moley, I. U. Mysorekar, G. R. Screaton and M. S. Diamond (2017). “Human antibodies to the dengue virus E-dimer epitope have therapeutic activity against Zika virus infection.” Nat Immunol 18(11): 1261-1269.
The Zika virus (ZIKV) epidemic has resulted in congenital abnormalities in fetuses and neonates. Although some cross-reactive dengue virus (DENV)-specific antibodies can enhance ZIKV infection in mice, those recognizing the DENV E-dimer epitope (EDE) can neutralize ZIKV infection in cell culture. We evaluated the therapeutic activity of human monoclonal antibodies to DENV EDE for their ability to control ZIKV infection in the brains, testes, placentas, and fetuses of mice. A single dose of the EDE1-B10 antibody given 3 d after ZIKV infection protected against lethality, reduced ZIKV levels in brains and testes, and preserved sperm counts. In pregnant mice, wild-type or engineered LALA variants of EDE1-B10, which cannot engage Fcg receptors, diminished ZIKV burden in maternal and fetal tissues, and protected against fetal demise. Because neutralizing antibodies to EDE have therapeutic potential against ZIKV, in addition to their established inhibitory effects against DENV, it may be possible to develop therapies that control disease caused by both viruses.
Emerging Infectious Diseases Vaccines
Magnani, D. M., C. G. T. Silveira, M. J. Ricciardi, L. Gonzalez-Nieto, N. Pedreno-Lopez, V. K. Bailey, M. J. Gutman, H. S. Maxwell, A. Domingues, P. R. Costa, L. Ferrari, R. Goulart, M. A. Martins, J. M. Martinez-Navio, S. P. Fuchs, J. Kalil, M. D. C. Timenetsky, J. Wrammert, S. S. Whitehead, D. R. Burton, R. C. Desrosiers, E. G. Kallas and D. I. Watkins (2017). “Potent Plasmablast-Derived Antibodies Elicited by the National Institutes of Health Dengue Vaccine.” J Virol 91(22).
Exposure to dengue virus (DENV) is thought to elicit lifelong immunity, mediated by DENV-neutralizing antibodies (nAbs). However, Abs generated by primary infections confer serotype-specific protection, and immunity against other serotypes develops only after subsequent infections. Accordingly, the induction of these nAb responses acquired after serial DENV infections has been a long-sought-after goal for vaccination. Nonetheless, it is still unclear if tetravalent vaccines can elicit or recall nAbs. In this study, we have characterized the responses from a volunteer who had been previously exposed to DENV and was immunized with the live attenuated tetravalent vaccine Butantan-DV, developed by the NIH and Butantan Institute. Eleven days after vaccination, we observed an approximately 70-fold expansion of the plasmablast population. We generated 21 monoclonal Abs (MAbs) from singly sorted plasmablasts. These MAbs were the result of clonal expansions and had significant levels of somatic hypermutation (SHM). Nineteen MAbs (90.5%) neutralized at least one DENV serotype at concentrations of 1 mug/ml or less; 6 of the 21 MAbs neutralized three or more serotypes. Despite the tetravalent composition of the vaccine, we observed a neutralization bias in the induced repertoire: DENV3 was targeted by 18 of the 19 neutralizing MAbs (nMAbs). Furthermore, the P3D05 nMAb neutralized DENV3 with extraordinary potency (concentration to achieve half-maximal neutralization [Neut50] = 0.03 mug/ml). Thus, the Butantan-DV vaccine engendered a mature, antigen-selected B cell repertoire. Our results suggest that preexisting responses elicited by a previous DENV3 infection were recalled by immunization. IMPORTANCE The dengue epidemic presents a global public health challenge that causes widespread economic burden and remains largely unchecked by existing control strategies. Successful control of the dengue epidemic will require effective prophylactic and therapeutic interventions. Several vaccine clinical efficacy trials are approaching completion, and the chances that one or more live attenuated tetravalent vaccines (LATVs) will be introduced worldwide is higher than ever. While it is widely accepted that dengue virus (DENV)-neutralizing antibody (nAb) titers are associated with protection, the Ab repertoire induced by LATVs remain uncharacterized. Here, we describe the isolation of potent (Neut50 < 0.1 mug/ml) nAbs from a DENV-seropositive volunteer immunized with the tetravalent vaccine Butantan-DV, which is currently in phase III trials.
Adhikari, U. K. and M. M. Rahman (2017). “Overlapping CD8+ and CD4+ T-cell epitopes identification for the progression of epitope-based peptide vaccine from nucleocapsid and glycoprotein of emerging Rift Valley fever virus using immunoinformatics approach.” Infect Genet Evol.
Rift Valley fever virus (RVFV) is an emergent arthropod-borne zoonotic infectious viral pathogen which causes fatal diseases in the humans and ruminants. Currently, no effective and licensed vaccine is available for the prevention of RVFV infection in endemic as well as in non-endemic regions. So, an immunoinformatics-driven genome-wide screening approach was performed for the identification of overlapping CD8+ and CD4+ T-cell epitopes and also linear B-cell epitopes from the conserved sequences of the nucleocapsid (N) and glycoprotein (G) of RVFV. We identified overlapping 99.39% conserved 1 CD8+ T-cell epitope (MMHPSFAGM) from N protein and 100% conserved 7 epitopes (AVFALAPVV, LAVFALAPV, FALAPVVFA, VFALAPVVF, IAMTVLPAL, FFDWFSGLM, and FLLIYLGRT) from G protein and also identified IL-4 and IFN-gamma induced (99.39% conserved) 1 N protein CD4+ T-cell epitope (HMMHPSFAGMVDPSL) and 100% conserved 5 G protein CD4+ T-cell epitopes (LPALAVFALAPVVFA, PALAVFALAPVVFAE, GIAMTVLPALAVFAL, GSWNFFDWFSGLMSW, and FFLLIYLGRTGLSKM). The overlapping CD8+ and CD4+ T-cell epitopes were bound with most conserved HLA-C*12:03 and HLA-DRB1*01:01, respectively with the high binding affinity (kcal/mol). The combined population coverage analysis revealed that the allele frequencies of these epitopes are high in endemic and non-endemic regions. Besides, we found 100% conserved and non-allergenic 2 decamer B-cell epitopes, GVCEVGVQAL and RVFNCIDWVH of G protein had the sequence similarity with the nonamer CD8+ T-cell epitopes, VCEVGVQAL and RVFNCIDWV, respectively. Consequently, these epitopes may be used for the development of epitope-based peptide vaccine against emerging RVFV. However, in vivo and in vitro experiments are required for their efficient use as a vaccine.
HIV- Acute Infection
Henrich, T. J., H. Hatano, O. Bacon, L. E. Hogan, R. Rutishauser, A. Hill, M. F. Kearney, E. M. Anderson, S. P. Buchbinder, S. E. Cohen, M. Abdel-Mohsen, C. W. Pohlmeyer, R. Fromentin, R. Hoh, A. Y. Liu, J. M. McCune, J. Spindler, K. Metcalf-Pate, K. S. Hobbs, C. Thanh, E. A. Gibson, D. R. Kuritzkes, R. F. Siliciano, R. W. Price, D. D. Richman, N. Chomont, J. D. Siliciano, J. W. Mellors, S. A. Yukl, J. N. Blankson, T. Liegler and S. G. Deeks (2017). “HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: An observational study.” PLoS Med 14(11): e1002417.
BACKGROUND: It is unknown if extremely early initiation of antiretroviral therapy (ART) may lead to long-term ART-free HIV remission or cure. As a result, we studied 2 individuals recruited from a pre-exposure prophylaxis (PrEP) program who started prophylactic ART an estimated 10 days (Participant A; 54-year-old male) and 12 days (Participant B; 31-year-old male) after infection with peak plasma HIV RNA of 220 copies/mL and 3,343 copies/mL, respectively. Extensive testing of blood and tissue for HIV persistence was performed, and PrEP Participant A underwent analytical treatment interruption (ATI) following 32 weeks of continuous ART. METHODS AND FINDINGS: Colorectal and lymph node tissues, bone marrow, cerebral spinal fluid (CSF), plasma, and very large numbers of peripheral blood mononuclear cells (PBMCs) were obtained longitudinally from both participants and were studied for HIV persistence in several laboratories using molecular and culture-based detection methods, including a murine viral outgrowth assay (mVOA). Both participants initiated PrEP with tenofovir/emtricitabine during very early Fiebig stage I (detectable plasma HIV-1 RNA, antibody negative) followed by 4-drug ART intensification. Following peak viral loads, both participants experienced full suppression of HIV-1 plasma viremia. Over the following 2 years, no further HIV could be detected in blood or tissue from PrEP Participant A despite extensive sampling from ileum, rectum, lymph nodes, bone marrow, CSF, circulating CD4+ T cell subsets, and plasma. No HIV was detected from tissues obtained from PrEP Participant B, but low-level HIV RNA or DNA was intermittently detected from various CD4+ T cell subsets. Over 500 million CD4+ T cells were assayed from both participants in a humanized mouse outgrowth assay. Three of 8 mice infused with CD4+ T cells from PrEP Participant B developed viremia (50 million input cells/surviving mouse), but only 1 of 10 mice infused with CD4+ T cells from PrEP Participant A (53 million input cells/mouse) experienced very low level viremia (201 copies/mL); sequence confirmation was unsuccessful. PrEP Participant A stopped ART and remained aviremic for 7.4 months, rebounding with HIV RNA of 36 copies/mL that rose to 59,805 copies/mL 6 days later. ART was restarted promptly. Rebound plasma HIV sequences were identical to those obtained during acute infection by single-genome sequencing. Mathematical modeling predicted that the latent reservoir size was approximately 200 cells prior to ATI and that only around 1% of individuals with a similar HIV burden may achieve lifelong ART-free remission. Furthermore, we observed that lymphocytes expressing the tumor marker CD30 increased in frequency weeks to months prior to detectable HIV-1 RNA in plasma. This study was limited by the small sample size, which was a result of the rarity of individuals presenting during hyperacute infection. CONCLUSIONS: We report HIV relapse despite initiation of ART at one of the earliest stages of acute HIV infection possible. Near complete or complete loss of detectable HIV in blood and tissues did not lead to indefinite ART-free HIV remission. However, the small numbers of latently infected cells in individuals treated during hyperacute infection may be associated with prolonged ART-free remission.
HIV – Cures & Treatments
Bunders, M. J. and M. Altfeld (2017). “Can NK cells purge HIV sanctuaries?” Nat Med 23(11): 1254-1255.
Spivak, A. M. and V. Planelles (2017). “Novel Latency Reversal Agents for HIV-1 Cure.” Annu Rev Med.
Antiretroviral therapy (ART) has rendered HIV-1 infection a treatable illness; however, ART is not curative owing to the persistence of replication-competent, latent proviruses in long-lived resting Tcells. Strategies that target these latently infected cells and allow immune recognition and clearance of this reservoir will be necessary to eradicate HIV-1 in infected individuals. This review describes current pharmacologic approaches to reactivate the latent reservoir so that infected cells can be recognized and targeted, with the ultimate goal of achieving an HIV-1 cure. Expected final online publication date for the Annual Review of Medicine Volume 69 is January 29, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Skaathun, B., A. S. Khanna, E. Morgan, S. R. Friedman and J. A. Schneider (2017). “Network Viral Load: A Critical Metric For HIV Elimination.” J Acquir Immune Defic Syndr.
BACKGROUND: Associations have been observed between an aggregate viral load measure, the community viral load (CVL) and new HIV diagnoses. The CVL aggregates viral loads within chosen geographic areas, restricting inferences about HIV acquisition risk to these areas. We develop a more precise metric, the Network Viral Load (NVL) to measure the composite viral load within a risk network of an HIV negative individual. METHODS: We examined the relationship between NVL and HIV infection among Young Men who have Sex with Men (YMSM) in Chicago, United States. Networks were generated using Respondent Driven Sampling. NVL was defined as the prevalence of viremic individuals in one’s risk network, characterized as those with a viral load >20k copies/mL. Permutation tests were conducted to account for dependency. RESULTS: After controlling for total connections, age, substance use during sex, syphilis diagnosis (previous 12 months), and frequency of condomless anal sex (previous 6 months), we found a positive association between NVL and HIV infection. Compared to a network with all HIV-seronegative members, the odds of HIV infection with a NVL of <10% viremia were 1.85 (95% C.I. 1.18-2.92) times higher and a NVL of >10% viremia were 2.73 (95% C.I. 1.54-4.85) times higher. CONCLUSION: We found a positive association between NVL and HIV seroprevalence. While limited in its ability to infer causality, NVL could have substantial public health implications for persons most at risk for HIV infection given that this novel metric avoids overreliance on individual level behavior or broad community indices.
Lavender, K. J., C. Pace, K. Sutter, R. J. Messer, D. L. Pouncey, N. W. Cummins, S. Natesampillai, J. Zheng, J. Goldsmith, M. Widera, E. S. Van Dis, K. Phillips, B. Race, U. Dittmer, G. Kukolj and K. J. Hasenkrug (2017). “An advanced BLT-humanized mouse model for extended HIV-1 cure studies.” Aids.
OBJECTIVE: Although BLT-humanized mice provide a robust model for HIV-1 infection and enable evaluation of cure strategies dependent on endogenous immune responses, most mice develop graft versus host disease (GVHD), limiting their utility for extended HIV cure studies. This study aimed to: 1) Evaluate the GVHD-resistant C57BL/6 Rag2gammacCD47 triple knockout (TKO)-BLT mouse as a model to establish HIV-1 latency. 2) Determine whether TKO-BLT mice could be maintained on ART for extended periods of time. 3) Assess the rapidity of viral rebound following therapy interruption. DESIGN: TKO-BLT mice were HIV-1 infected, treated with various ART regimens over extended periods of time and assayed for viral rebound following therapy interruption. METHODS: Daily subcutaneous injection and oral ART-mediated suppression of HIV-1 infection was tested at various doses in TKO-BLT mice. Mice were monitored for suppression of viremia and cellular HIV-1 RNA and DNA prior to and following therapy interruption. RESULTS: Mice remained healthy for 45 weeks post-humanization and could be treated with ART for up to 18 weeks. Viremia was suppressed to < 200 copies/ml in the majority of mice with significant reductions in cellular HIV-1 RNA and DNA. Treatment interruption resulted in rapid viral recrudescence. CONCLUSIONS: HIV-1 latency can be maintained in TKO-BLT mice over extended periods on ART and rapid viral rebound occurs following therapy removal. The additional 15-18 weeks of healthy longevity compared to other BLT models provides sufficient time to examine the decay kinetics of the latent reservoir as well as observe delays in recrudescence in HIV-1 cure studies.
HIV – HLA
Leitman, E. M., C. B. Willberg, M. H. Tsai, H. Chen, S. Buus, F. Chen, L. Riddell, D. Haas, J. Fellay, J. J. Goedert, A. Piechocka-Trocha, B. D. Walker, J. Martin, S. Deeks, S. M. Wolinsky, J. Martinson, M. Martin, Y. Qi, A. Saez-Cirion, O. O. Yang, P. C. Matthews, M. Carrington and P. J. R. Goulder (2017). “HLA-B*14:02-Restricted Env-Specific CD8+ T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection.” J Virol 91(22).
Immune control of human immunodeficiency virus type 1 (HIV) infection is typically associated with effective Gag-specific CD8+ T-cell responses. We here focus on HLA-B*14, which protects against HIV disease progression, but the immunodominant HLA-B*14-restricted anti-HIV response is Env specific (ERYLKDQQL, HLA-B*14-EL9). A subdominant HLA-B*14-restricted response targets Gag (DRYFKTLRA, HLA-B*14-DA9). Using HLA-B*14/peptide-saporin-conjugated tetramers, we show that HLA-B*14-EL9 is substantially more potent at inhibiting viral replication than HLA-B*14-DA9. HLA-B*14-EL9 also has significantly higher functional avidity (P < 0.0001) and drives stronger selection pressure on the virus than HLA-B*14-DA9. However, these differences were HLA-B*14 subtype specific, applying only to HLA-B*14:02 and not to HLA-B*14:01. Furthermore, the HLA-B*14-associated protection against HIV disease progression is significantly greater for HLA-B*14:02 than for HLA-B*14:01, consistent with the superior antiviral efficacy of the HLA-B*14-EL9 response. Thus, although Gag-specific CD8+ T-cell responses may usually have greater anti-HIV efficacy, factors independent of protein specificity, including functional avidity of individual responses, are also critically important to immune control of HIV.IMPORTANCE In HIV infection, although cytotoxic T lymphocytes (CTL) play a potentially critical role in eradication of viral reservoirs, the features that constitute an effective response remain poorly defined. We focus on HLA-B*14, unique among HLAs associated with control of HIV in that the dominant CTL response is Env specific, not Gag specific. We demonstrate that Env-specific HLA-B*14-restricted activity is substantially more efficacious than the subdominant HLA-B*14-restricted Gag response. Env immunodominance over Gag and strong Env-mediated selection pressure on HIV are observed only in subjects expressing HLA-B*14:02, and not HLA-B*14:01. This reflects the increased functional avidity of the Env response over Gag, substantially more marked for HLA-B*14:02. Finally, we show that HLA-B*14:02 is significantly more strongly associated with viremic control than HLA-B*14:01. These findings indicate that, although Gag-specific CTL may usually have greater anti-HIV efficacy than Env responses, factors independent of protein specificity, including functional avidity, may carry greater weight in mediating effective control of HIV.
Soto-Nava, M., S. Avila-Rios, H. Valenzuela-Ponce, C. Garcia-Morales, J. M. Carlson, D. Tapia-Trejo, D. Garrido-Rodriguez, S. N. Alva-Hernandez, T. A. Garcia-Tellez, A. Murakami-Ogasawara, S. A. Mallal, M. John, M. A. Brockman, C. J. Brumme, Z. L. Brumme and G. Reyes-Teran (2017). “Weaker HLA footprints on HIV in the unique and highly genetically admixed host population of Mexico.” J Virol.
HIV circumvents HLA class I-restricted CD8+ T cell responses through selection of escape mutations that leave characteristic mutational “footprints” – also known as HLA-associated polymorphisms (HAPs) – on HIV sequences at the population level. While many HLA footprints are universal across HIV subtypes and human populations, others can be region-specific as a result of the unique immunogenetic background of each host population. Using a published probabilistic phylogenetically-informed model, we compared HAPs in HIV Gag and Pol (PR-RT) in 1,612 subtype B-infected, antiretroviral treatment-naive individuals from Mexico and 1,641 from Canada/USA. A total of 252 HLA class I allele subtypes were represented, including 140 observed in both cohorts, 67 unique to Mexico and 45 unique to Canada/USA. At the predefined statistical threshold of q<0.2, 358 HAPs (201 in Gag; 157 in PR-RT) were identified in Mexico, while 905 (534 in Gag and 371 in PR-RT) were identified in Canada/USA. HAP identified in Mexico included both “canonical” HLA-associated escape pathways and novel associations, in particular with HLA alleles enriched in Amerindian and mestizo populations. Remarkably, HLA footprints on HIV in Mexico were not only fewer but also on average significantly weaker than those in Canada/USA, though some exceptions were noted. Moreover, exploratory analyses suggested that the weaker HLA footprint on HIV in Mexico may be due, at least in part, to weaker and/or less reproducible HLA-mediated immune pressures on HIV in this population. The implications of these differences for natural and vaccine-induced anti-HIV immunity merit further investigation. IMPORTANCEHLA footprints on HIV identify viral regions under intense and consistent pressure by HLA-restricted immune responses and the common mutational pathways that HIV uses to evade them. In particular, HLA footprints can identify novel immunogenic regions and/or epitopes targeted by understudied HLA alleles; moreover, comparative analyses across immunogenetically distinct populations can illuminate the extent to which HIV immunogenic regions and escape pathways are shared versus population-specific, information which can in turn inform the design of universal or geographically-tailored HIV vaccines. We compared HLA-associated footprints on HIV in two immunogenetically distinct North American populations – Mexico and Canada/USA. We identify both shared and population-specific pathways of HIV adaptation, but also make the surprising observation that HLA footprints on HIV in Mexico are overall fewer and weaker than in Canada/USA, raising the possibility that HLA-restricted antiviral immune responses in Mexico may be weaker, and/or escape pathways somewhat less consistent, than in other populations.
HIV – Passive Immunization
Ruprecht, R. M. (2017). “Anti-HIV Passive Immunization: New Weapons in the Arsenal.” Trends Microbiol.
Anti-HIV passive immunization with human neutralizing monoclonal antibodies (nmAbs) has made exciting gains: (i) identification of the HIV envelope V2 apex as a new in vivo protective epitope, (ii) a novel clade C SHIV for challenge studies, and (iii) a highly protective, trispecific nmAb. Potent, broad-spectrum protection by nmAbs holds promise.
HIV – Pathogenesis & Disease Progression
Fenoglio, D., C. Dentone, A. Signori, A. Di Biagio, A. Parodi, F. Kalli, G. Nasi, M. Curto, G. Cenderello, P. De Leo, V. Bartolacci, G. Orofino, L. A. Nicolini, L. Taramasso, E. Fiorillo, V. Orru, P. Traverso, B. Bruzzone, F. Ivaldi, E. Mantia, M. Guerra, S. Negrini, M. Giacomini, S. Bhagani and G. Filaci (2017). “CD8+CD28-CD127loCD39+ regulatory T-cell expansion: A new possible pathogenic mechanism for HIV infection?” J Allergy Clin Immunol.
BACKGROUND: HIV-associated immunodeficiency is related to loss of CD4+ T cells. This mechanism does not explain certain manifestations of HIV disease, such as immunodeficiency events in patients with greater than 500 CD4+ T cells/muL. CD8+CD28-CD127loCD39+ T cells are regulatory T (Treg) lymphocytes that are highly concentrated within the tumor microenvironment and never analyzed in the circulation of HIV-infected patients. OBJECTIVES: We sought to analyze the frequency of CD8+CD28-CD127loCD39+ Treg cells in the circulation of HIV-infected patients. METHODS: The frequency of circulating CD8+CD28-CD127loCD39+ Treg cells was analyzed and correlated with viral load and CD4+ T-cell counts/percentages in 93 HIV-1-infected patients subdivided as follows: naive (n = 63), elite controllers (n = 19), long-term nonprogressors (n = 7), and HIV-infected patients affected by tumor (n = 4). The same analyses were performed in HIV-negative patients with cancer (n = 53), hepatitis C virus-infected patients (n = 17), and healthy donors (n = 173). RESULTS: HIV-infected patients had increased circulating levels of functional CD8+CD28-CD127loCD39+ Treg cells. These cells showed antigen specificity against HIV proteins. Their frequency after antiretroviral therapy (ART) correlated with HIV viremia, CD4+ T-cell counts, and immune activation markers, suggesting their pathogenic involvement in AIDS- or non-AIDS-related complications. Their increase after initiation of ART heralded a lack of virologic or clinical response, and hence their monitoring is clinically relevant. CONCLUSION: HIV infection induces remarkable expansion of CD8+CD28-CD127loCD39+ Treg cells, the frequency of which correlates with both clinical disease and signs of chronic immune cell activation. Monitoring their frequency in the circulation is a new marker of response to ART when effects on viremia and clinical response are not met.
Blees, A., D. Januliene, T. Hofmann, N. Koller, C. Schmidt, S. Trowitzsch, A. Moeller and R. Tampe (2017). “Structure of the human MHC-I peptide-loading complex. “Nature.
The peptide-loading complex (PLC) is a transient, multisubunit membrane complex in the endoplasmic reticulum that is essential for establishing a hierarchical immune response. The PLC coordinates peptide translocation into the endoplasmic reticulum with loading and editing of major histocompatibility complex class I (MHC-I) molecules. After final proofreading in the PLC, stable peptide-MHC-I complexes are released to the cell surface to evoke a T-cell response against infected or malignant cells. Sampling of different MHC-I allomorphs requires the precise coordination of seven different subunits in a single macromolecular assembly, including the transporter associated with antigen processing (TAP1 and TAP2, jointly referred to as TAP), the oxidoreductase ERp57, the MHC-I heterodimer, and the chaperones tapasin and calreticulin. The molecular organization of and mechanistic events that take place in the PLC are unknown owing to the heterogeneous composition and intrinsically dynamic nature of the complex. Here, we isolate human PLC from Burkitt’s lymphoma cells using an engineered viral inhibitor as bait and determine the structure of native PLC by electron cryo-microscopy. Two endoplasmic reticulum-resident editing modules composed of tapasin, calreticulin, ERp57, and MHC-I are centred around TAP in a pseudo-symmetric orientation. A multivalent chaperone network within and across the editing modules establishes the proofreading function at two lateral binding platforms for MHC-I molecules. The lectin-like domain of calreticulin senses the MHC-I glycan, whereas the P domain reaches over the MHC-I peptide-binding pocket towards ERp57. This arrangement allows tapasin to facilitate peptide editing by clamping MHC-I. The translocation pathway of TAP opens out into a large endoplasmic reticulum lumenal cavity, confined by the membrane entry points of tapasin and MHC-I. Two lateral windows channel the antigenic peptides to MHC-I. Structures of PLC captured at distinct assembly states provide mechanistic insight into the recruitment and release of MHC-I. Our work defines the molecular symbiosis of an ABC transporter and an endoplasmic reticulum chaperone network in MHC-I assembly and provides insight into the onset of the adaptive immune response.
Blachere, N. E., D. E. Orange, E. C. Gantman, B. D. Santomasso, G. C. Couture, T. Ramirez-Montagut, J. Fak, K. J. O’Donovan, Z. Ru, S. Parveen, M. O. Frank, M. J. Moore and R. B. Darnell (2017). “T cells presenting viral antigens or autoantigens induce cytotoxic T cell anergy.” JCI Insight 2(21).
In the course of modeling the naturally occurring tumor immunity seen in patients with paraneoplastic cerebellar degeneration (PCD), we discovered an unexpectedly high threshold for breaking CD8+ cytotoxic T cell (CTL) tolerance to the PCD autoantigen, CDR2. While CDR2 expression was previously found to be strictly restricted to immune-privileged cells (cerebellum, testes, and tumors), unexpectedly we have found that T cells also express CDR2. This expression underlies inhibition of CTL activation; CTLs that respond to epithelial cells expressing CDR2 fail to respond to T cells expressing CDR2. This was a general phenomenon, as T cells presenting influenza (flu) antigen also fail to activate otherwise potent flu-specific CTLs either in vitro or in vivo. Moreover, transfer of flu peptide-pulsed T cells into flu-infected mice inhibits endogenous flu-specific CTLs. Our finding that T cells serve as a site of immune privilege, inhibiting effector CTL function, uncovers an autorepressive loop with general biologic and clinical relevance.
Heleen van den Heuvel, H., K. M. Heutinck, E. M. W. van der Meer-Prins, M. E. I. Franke-van Dijk, P. van Miert, X. Zhang, I. J. M. Ten Berge and F. H. J. Claas (2017). “The Avidity of Cross-Reactive Virus-Specific T Cells for their Viral and Allogeneic Epitopes is Variable and Depends on Epitope Expression.” Hum Immunol.
Virus-specific T cells can recognize allogeneic HLA (allo-HLA) through cross-reactivity of their T-cell receptor (TCR). In a transplantation setting, such allo-HLA cross-reactivity may contribute to harmful immune responses towards the allograft, provided that the cross-reactive T cells get sufficiently activated upon recognition of the allo-HLA. An important determinant of T-cell activation is TCR avidity, which to date, has remained largely unexplored for allo-HLA-cross-reactive virus-specific T cells. For this purpose, cold target inhibition assays were performed using allo-HLA-cross-reactive virus-specific memory CD8+ T-cell clones as responders, and syngeneic cells loaded with viral peptide and allogeneic cells as hot (radioactively-labeled) and cold (non-radioactively-labeled) targets. CD8 dependency of the T-cell responses was assessed using interferon gamma (IFNgamma) enzyme-linked immunosorbent assay (ELISA) in the presence and absence of CD8-blocking antibodies. At high viral-peptide loading concentrations, T-cell clones consistently demonstrated lower avidity for allogeneic versus viral epitopes, but at suboptimal concentrations the opposite was observed. In line, anti-viral reactivity was CD8 independent at high, but not at suboptimal viral-peptide-loading concentrations. The avidity of allo-HLA-cross-reactive virus-specific memory CD8+ T cells is therefore highly dependent on epitope expression, and as a consequence, can be both higher and lower for allogeneic versus viral targets under different (patho)physiological conditions.
Muller, M., D. Gfeller, G. Coukos and M. Bassani-Sternberg (2017). “‘Hotspots’ of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization.” Front Immunol 8: 1367.
The remarkable clinical efficacy of the immune checkpoint blockade therapies has motivated researchers to discover immunogenic epitopes and exploit them for personalized vaccines. Human leukocyte antigen (HLA)-binding peptides derived from processing and presentation of mutated proteins are one of the leading targets for T-cell recognition of cancer cells. Currently, most studies attempt to identify neoantigens based on predicted affinity to HLA molecules, but the performance of such prediction algorithms is rather poor for rare HLA class I alleles and for HLA class II. Direct identification of neoantigens by mass spectrometry (MS) is becoming feasible; however, it is not yet applicable to most patients and lacks sensitivity. In an attempt to capitalize on existing immunopeptidomics data and extract information that could complement HLA-binding prediction, we first compiled a large HLA class I and class II immunopeptidomics database across dozens of cell types and HLA allotypes and detected hotspots that are subsequences of proteins frequently presented. About 3% of the peptidome was detected in both class I and class II. Based on the gene ontology of their source proteins and the peptide’s length, we propose that their processing may partake by the cellular class II presentation machinery. Our database captures the global nature of the in vivo peptidome averaged over many HLA alleles, and therefore, reflects the propensity of peptides to be presented on HLA complexes, which is complementary to the existing neoantigen prediction features such as binding affinity and stability or RNA abundance. We further introduce two immunopeptidomics MS-based features to guide prioritization of neoantigens: the number of peptides matching a protein in our database and the overlap of the predicted wild-type peptide with other peptides in our database. We show as a proof of concept that our immunopeptidomics MS-based features improved neoantigen prioritization by up to 50%. Overall, our work shows that, in addition to providing huge training data to improve the HLA binding prediction, immunopeptidomics also captures other aspects of the natural in vivo presentation that significantly improve prediction of clinically relevant neoantigens.
Marjoram, D., Y. Cruz-Leal, L. Bernardo, N. P. L. Le, M. Crispin, X. Yu, M. Uchikawa and A. H. Lazarus (2017). “Immunoglobulin G Fc glycans are not essential for antibody-mediated immune suppression to murine erythrocytes.” Blood.
Vaccine Design Immunogenicity Efficacy
Arnold, C. (2017). “Stalking new vaccines: Methods that target the stems of viral proteins could put universal vaccines within reach.” Nat Med 23(11): 1248-1250.
Yan, J., M. P. Morrow, J. S. Chu, T. Racine, C. C. Reed, A. S. Khan, K. E. Broderick, J. J. Kim, G. P. Kobinger, N. Y. Sardesai and D. B. Weiner (2017). “Broad cross-protective anti-hemagglutination responses elicited by influenza microconsensus DNA vaccine.” Vaccine.
Despite the routine development and distribution of seasonal influenza vaccines, influenza remains an important pathogen contributing to significant human morbidity as well as mortality each year. The seasonal variability of influenza creates a significant issue for vaccine development of seasonal strains that can afford protection from infection or disease based on serotype matching. It is appreciated that the globular head of the HA antigen contained in the vaccines generates antibodies that result in HAI activity that are a major correlates of the protection against a particular strain. Due to seasonal genetic changes in the HA protein, however, new vaccine strains are needed to be developed continually to match the new HA antigen of that seasons virus. A distinct advantage in seasonal vaccine development would be if a small group of antigens could be developed that could span many seasons without needed to be replaced due to this genetic drift. Here we report on a synthetic microconsensus approach that relies on a small collection of 4 synthetic H1HA DNA antigens which together induce broad protective HAI immunity spanning decades of H1 influenza viruses in mice, guinea pigs and non-human primates. The protective HAI titers induced by microconsensus immunogens are fully functional in vivo as immunized ferrets were completely protected from A/Mexico/InDRE4487/2009 virus infection and morbidity associated with lethal challenge. These results are encouraging that a limited easy-to-formulate collection of invariant antigens can be developed which can span seasonal vaccine changes allowing for continued immune protection.
Reeves, P. M., A. E. Sluder, S. R. Paul, A. Scholzen, S. Kashiwagi and M. C. Poznansky (2017). “Application and utility of mass cytometry in vaccine development.” Faseb j.
Mass cytometry enables highly multiplexed profiling of cellular immune responses in limited-volume samples, advancing prospects of a new era of systems immunology. The capabilities of mass cytometry offer expanded potential for deciphering immune responses to infectious diseases and to vaccines. Several studies have used mass cytometry to profile protective immune responses, both postinfection and postvaccination, although no vaccine-development program has yet systematically employed the technology from the outset to inform both candidate design and clinical evaluation. In this article, we review published mass cytometry studies relevant to vaccine development, briefly compare immune profiling by mass cytometry to other systems-level technologies, and discuss some general considerations for deploying mass cytometry in the context of vaccine development.
Pradhan, D., M. Yadav, R. Verma, N. S. Khan, L. Jena and A. K. Jain (2017). “Discovery of T-cell Driven Subunit Vaccines from Zika Virus Genome: An Immunoinformatics Approach.” Interdiscip Sci.
The recent outbreaks of Zika virus and the absence of a specific therapy have necessitated to identify T-cell-stimulating antigenic peptides as potential subunit vaccine candidates. The translated ssRNA (+) genome of Zika virus was explored in EMBOSS antigenic and VaxiJen to predict 63 peptides as potential antigens. Three MHC-II binding peptide prediction tools, viz. NetMHCIIpan, PREDIVAC and immune epitope database (IEDB) were employed in consensus on 63 antigenic peptides to propose 14 T-helper cell epitopes. Similarly, analysis on 63 antigenic peptides through NetMHC, NetCTL and IEDB MHC-I binding peptide prediction tool led to identification of 14 CTL epitopes. Seven T-cell epitopes, C:44-66, M:135-149, NS2A:124-144, NS3:421-453, NS3:540-554, NS4B:90-134 and NS4B:171-188, are observed to share overlapping MHC-I and MHC-II binding motifs and hence, are being proposed to constitute minimum T-cell antigens to elicit protective T-cell immune response against Zika. Three of them, C:44-66, NS3:421-453 and NS3:540-554 are identified to be conserved across all the selected strains of Zika virus. Moreover, the 21 T-cell epitopes are non-self to humans and exhibited good coverage in variable populations of 14 geographical locations. Therefore, 21 T-cell epitopes are proposed as potential subunit vaccines against Zika virus.