AIDS Vaccine Design Immunogenicity Efficacy
Dorta-Estremera, S., P. N. Nehete, G. Yang, H. He, B. P. Nehete, K. K. Shelton, M. A. Barry and K. J. Sastry (2017). “Minimally invasive monitoring of CD4 T cells at multiple mucosal tissues after intranasal vaccination in rhesus macaques.” PLoS One 12(12): e0188807.
Studies in nonhuman primates (NHP) for prospective immune cell monitoring subsequent to infection and/or vaccination usually rely on periodic sampling of the blood samples with only occasional collections of biopsies from mucosal tissues because of safety concerns and practical constraints. Here we present evidence in support of cytobrush sampling of oral, rectal, and genital mucosal tissues as a minimally invasive approach for the phenotypic analyses of different T cells subsets de novo as well as prospectively after intranasal immunization in rhesus macaques. Significant percentages of viable lymphocytes were obtained consistently from both naive and chronically SIV-infected rhesus macaques. The percentages of CD3+ T cells in the blood were significantly higher compared to those in the mucosal tissues analyzed in the naive animals, while in the SIV+ animals the CD3+ T cells were significantly elevated in the rectal tissues, relative to all other sites analyzed. In the naive, but not SIV+ macaques, the rectal and vaginal mucosal tissues, compared to oral mucosa and blood, showed higher diversity and percentages of CD4+ T cells expressing the HIV entry co-receptor CCR5 and mucosal specific adhesion (CD103) as well as activation (HLA-DR) and proliferation (Ki67) markers. Sequential daily cytobrush sampling from the oral, rectal, and genital mucosal tissues was performed in SIV+ animals from an ongoing study where they were administered intranasal immunization with adenoviral vectored vaccines incorporating the green fluorescent protein (GFP) reporter gene. We detected a transient increase in GFP+ CD4 T cells in only oral mucosa suggesting limited mucosal trafficking. In general, CD4+ and CD8+ T cells expressing Ki67 transiently increased in all mucosal tissues, but those expressing the CCR5, HLA-DR, and CD103 markers exhibited minor changes. We propose the minimally invasive cytobrush sampling as a practical approach for effective and prospective immune monitoring of the oral-genital mucosal tissues in NHP.
Sahay, B., C. Q. Nguyen and J. K. Yamamoto (2017). “Conserved HIV Epitopes for an Effective HIV Vaccine.” J Clin Cell Immunol 8(4).
Despite major advances in antiretroviral therapy against HIV-1, an effective HIV vaccine is urgently required to reduce the number of new cases of HIV infections in the world. Vaccines are the ultimate tool in the medical arsenal to control and prevent the spread of infectious diseases such as HIV/AIDS. Several failed phase-IIb to -III clinical vaccine trials against HIV-1 in the past generated a plethora of information that could be used for better designing of an effective HIV vaccine in the future. Most of the tested vaccine candidates produced strong humoral responses against the HIV proteins; however, failed to protect due to: 1) the low levels and the narrow breadth of the HIV-1 neutralizing antibodies and the HIV-specific antibody-dependent Fc-mediated effector activities, 2) the low levels and the poor quality of the anti-HIV T-cell responses, and 3) the excessive responses to immunodominant non-protective HIV epitopes, which in some cases blocked the protective immunity and/or enhanced HIV infection. The B-cell epitopes on HIV for producing broadly neutralizing antibodies (bNAbs) against HIV have been extensively characterized, and the next step is to develop bNAb epitope immunogen for HIV vaccine. The bNAb epitopes are often conformational epitopes and therefore more difficult to construct as vaccine immunogen and likely to include immunodominant non-protective HIV epitopes. In comparison, T-cell epitopes are short linear peptides which are easier to construct into vaccine immunogen free of immunodominant non-protective epitopes. However, its difficulty lies in identifying the T-cell epitopes conserved among HIV subtypes and induce long-lasting, potent polyfunctional T-cell and cytotoxic T lymphocyte (CTL) activities against HIV. In addition, these protective T-cell epitopes must be recognized by the HLA prevalent in the country(s) targeted for the vaccine trial. In conclusion, extending from the findings from previous vaccine trials, future vaccines should combine both T- and B-cell epitopes as vaccine immunogen to induce multitude of broad and potent immune effector activities required for sterilizing protection against global HIV subtypes.
AIDS Vaccine Envelope Design
Steven W. de Taeye, S. W., A. Torrents de la Pena, A. Vecchione, E. Scutigliani, K. Sliepen, J. A. Burger, P. van der Woude, A. Schorcht, E. E. Schermer, M. J. van Gils, C. C. LaBranche, D. C. Montefiori, I. A. Wilson, J. P. Moore, A. B. Ward and R. W. Sanders (2017). “Stabilization of the gp120 V3 loop through hydrophobic interactions reduces the immunodominant V3-directed non-neutralizing response to HIV-1 envelope trimers.” J Biol Chem.
To provide protective immunity against circulating primary HIV-1 strains, a vaccine most likely has to induce broadly neutralizing antibodies (bNAbs) to the HIV-1 envelope (Env) glycoprotein spike. Recombinant Env trimers such as the prototype BG505 SOSIP.664 that closely mimic the native Env spike can induce autologous neutralizing antibodies (NAbs) against relatively resistant (tier-2) primary viruses. Ideally, Env immunogens should present bNAb epitopes, but limit the presentation of immunodominant non-NAb epitopes that might induce off-target and potentially interfering responses. The V3 loop in gp120 is such a non-NAb epitope that can effectively elicit non-NAbs when animals are immunized with SOSIP.664 trimers. V3 immunogenicity can be diminished, but not abolished, by reducing the conformational flexibility of trimers via targeted sequence changes, including an A316W substitution in V3, that create the SOSIP.v4.1 and SOSIP.v5.2 variants. Here, we further modified these trimer designs by introducing leucine residues at V3 positions 306 and 308 to create hydrophobic interactions with the tryptophan residue at position 316 and with other topologically proximal sites in the V1V2 domain. Together, these modifications further stabilized the resulting SOSIP.v5.2 S306L R308L trimers in the prefusion state in which V3 is sequestered. When we tested these trimers as immunogens in rabbits, the induction of V3 non-NAbs was significantly reduced compared with the SOSIP.v5.2 trimers and even more so compared with the SOSIP.664 prototype, without affecting the autologous NAb response. Hence, these additional trimer sequence modifications may be beneficial for immunization strategies that seek to minimize off-target non-NAb responses.
Emerging Infectious Diseases
Rimoin, A. W., K. Lu, M. S. Bramble, I. Steffen, R. H. Doshi, N. A. Hoff, P. Mukadi, B. P. Nicholson, V. H. Alfonso, G. Olinger, C. Sinai, L. K. Yamamoto, C. M. Ramirez, E. Okitolonda Wemakoy, B. Kebela Illunga, J. Pettitt, J. Logue, R. S. Bennett, P. Jahrling, D. L. Heymann, P. Piot, J. J. Muyembe-Tamfum, L. E. Hensley and G. Simmons (2017). “Ebola Virus Neutralizing Antibodies Detectable in Survivors of theYambuku, Zaire Outbreak 40 Years after Infection.” The Journal of Infectious Diseases: jix584-jix584.
The first reported outbreak of Ebola virus disease occurred in 1976 in Yambuku, Democratic Republic of Congo. Antibody responses in survivors 11 years after infection have been documented. However, this report is the first characterization of anti-Ebola virus antibody persistence and neutralization capacity 40 years after infection. Using ELISAs we measured survivor’s immunological response to Ebola virus Zaire (EBOV) glycoprotein and nucleoprotein, and assessed VP40 reactivity. Neutralization of EBOV was measured using a pseudovirus approach and plaque reduction neutralization test with live EBOV. Some survivors from the original EBOV outbreak still harbor antibodies against all 3 measures. Interestingly, a subset of these survivors’ serum antibodies could still neutralize live virus 40 years postinitial infection. These data provide the longest documentation of both anti-Ebola serological response and neutralization capacity within any survivor cohort, extending the known duration of response from 11 years postinfection to at least 40 years after symptomatic infection.
Benedict, K., M. Richardson, S. Vallabhaneni, B. R. Jackson and T. Chiller (2017). “Emerging issues, challenges, and changing epidemiology of fungal disease outbreaks.” Lancet Infect Dis 17(12): e403-e411.
Several high-profile outbreaks have drawn attention to invasive fungal infections (IFIs) as an increasingly important public health problem. IFI outbreaks are caused by many different fungal pathogens and are associated with numerous settings and sources. In the community, IFI outbreaks often occur among people without predisposing medical conditions and are frequently precipitated by environmental disruption. Health-care-associated IFI outbreaks have been linked to suboptimal hospital environmental conditions, transmission via health-care workers’ hands, contaminated medical products, and transplantation of infected organs. Outbreak investigations provide important insights into the epidemiology of IFIs, uncover risk factors for infection, and identify opportunities for preventing similar events in the future. Well recognised challenges with IFI outbreak recognition, response, and prevention include the need for improved rapid diagnostic methods, the absence of routine surveillance for most IFIs, adherence to infection control practices, and health-care provider awareness. Additionally, IFI outbreak investigations have revealed several emerging issues, including new populations at risk because of travel or relocation, occupation, or immunosuppression; fungal pathogens appearing in geographical areas in which they have not been previously recognised; and contaminated compounded medications. This report highlights notable IFI outbreaks in the past decade, with an emphasis on these emerging challenges in the USA.
Keller, J. I., B. A. Ballif, R. M. St Clair, J. J. Vincent, M. C. Monroy and L. Stevens (2017). “Chagas disease vector blood meal sources identified by protein mass spectrometry.” PLoS One 12(12): e0189647.
Chagas disease is a complex vector borne parasitic disease involving blood feeding Triatominae (Hemiptera: Reduviidae) insects, also known as kissing bugs, and the vertebrates they feed on. This disease has tremendous impacts on millions of people and is a global health problem. The etiological agent of Chagas disease, Trypanosoma cruzi (Kinetoplastea: Trypanosomatida: Trypanosomatidae), is deposited on the mammalian host in the insect’s feces during a blood meal, and enters the host’s blood stream through mucous membranes or a break in the skin. Identifying the blood meal sources of triatomine vectors is critical in understanding Chagas disease transmission dynamics, can lead to identification of other vertebrates important in the transmission cycle, and aids management decisions. The latter is particularly important as there is little in the way of effective therapeutics for Chagas disease. Several techniques, mostly DNA-based, are available for blood meal identification. However, further methods are needed, particularly when sample conditions lead to low-quality DNA or to assess the risk of human cross-contamination. We demonstrate a proteomics-based approach, using liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify host-specific hemoglobin peptides for blood meal identification in mouse blood control samples and apply LC-MS/MS for the first time to Triatoma dimidiata insect vectors, tracing blood sources to species. In contrast to most proteins, hemoglobin, stabilized by iron, is incredibly stable even being preserved through geologic time. We compared blood stored with and without an anticoagulant and examined field-collected insect specimens stored in suboptimal conditions such as at room temperature for long periods of time. To our knowledge, this is the first study using LC-MS/MS on field-collected arthropod disease vectors to identify blood meal composition, and where blood meal identification was confirmed with more traditional DNA-based methods. We also demonstrate the potential of synthetic peptide standards to estimate relative amounts of hemoglobin acquired when insects feed on multiple blood sources. These LC-MS/MS methods can contribute to developing Ecohealth control strategies for Chagas disease transmission and can be applied to other arthropod disease vectors.
Emerging Infectious Disease Vaccines
Black, S. (2018). “Editor’s Commentary: Vaccines as a Tool to Combat Antibiotic Resistance.” Pediatr Infect Dis J 37(1): 96.
Blackman, M. A., I. J. Kim, J. S. Lin and S. J. Thomas (2017). “Challenges of Vaccine Development for Zika Virus.” Viral Immunol.
The emergence of outbreaks of Zika virus (ZIKV) in Brazil in 2015 was associated with devastating effects on fetal development and prompted a world health emergency and multiple efforts to generate an effective vaccine against infection. There are now more than 40 vaccine candidates in preclinical development and six in clinical trials. Despite similarities with other flaviviruses to which successful vaccines have been developed, such as yellow fever virus and Japanese Encephalitis virus, there are unique challenges to the development and clinical trials of a vaccine for ZIKV.
Gaudinski, M. R., K. V. Houser, K. M. Morabito, Z. Hu, G. Yamshchikov, R. S. Rothwell, N. Berkowitz, F. Mendoza, J. G. Saunders, L. Novik, C. S. Hendel, L. A. Holman, I. J. Gordon, J. H. Cox, S. Edupuganti, M. A. McArthur, N. G. Rouphael, K. E. Lyke, G. E. Cummings, S. Sitar, R. T. Bailer, B. M. Foreman, K. Burgomaster, R. S. Pelc, D. N. Gordon, C. R. DeMaso, K. A. Dowd, C. Laurencot, R. M. Schwartz, J. R. Mascola, B. S. Graham, T. C. Pierson, J. E. Ledgerwood, G. L. Chen, Vrc and V. R. C. s. teams (2017). “Safety, tolerability, and immunogenicity of two Zika virus DNA vaccine candidates in healthy adults: randomised, open-label, phase 1 clinical trials.” Lancet.
BACKGROUND: The Zika virus epidemic and associated congenital infections have prompted rapid vaccine development. We assessed two new DNA vaccines expressing premembrane and envelope Zika virus structural proteins. METHODS: We did two phase 1, randomised, open-label trials involving healthy adult volunteers. The VRC 319 trial, done in three centres, assessed plasmid VRC5288 (Zika virus and Japanese encephalitis virus chimera), and the VRC 320, done in one centre, assessed plasmid VRC5283 (wild-type Zika virus). Eligible participants were aged 18-35 years in VRC19 and 18-50 years in VRC 320. Participants were randomly assigned 1:1 by a computer-generated randomisation schedule prepared by the study statistician. All participants received intramuscular injection of 4 mg vaccine. In VRC 319 participants were assigned to receive vaccinations via needle and syringe at 0 and 8 weeks, 0 and 12 weeks, 0, 4, and 8 weeks, or 0, 4, and 20 weeks. In VRC 320 participants were assigned to receive vaccinations at 0, 4, and 8 weeks via single-dose needle and syringe injection in one deltoid or split-dose needle and syringe or needle-free injection with the Stratis device (Pharmajet, Golden, CO, USA) in each deltoid. Both trials followed up volunteers for 24 months for the primary endpoint of safety, assessed as local and systemic reactogenicity in the 7 days after each vaccination and all adverse events in the 28 days after each vaccination. The secondary endpoint in both trials was immunogenicity 4 weeks after last vaccination. These trials are registered with ClinicalTrials.gov, numbers NCT02840487 and NCT02996461. FINDINGS: VRC 319 enrolled 80 participants (20 in each group), and VRC 320 enrolled 45 participants (15 in each group). One participant in VRC 319 and two in VRC 320 withdrew after one dose of vaccine, but were included in the safety analyses. Both vaccines were safe and well tolerated. All local and systemic symptoms were mild to moderate. In both studies, pain and tenderness at the injection site was the most frequent local symptoms (37 [46%] of 80 participants in VRC 319 and 36 [80%] of 45 in VRC 320) and malaise and headache were the most frequent systemic symptoms (22 [27%] and 18 [22%], respectively, in VRC 319 and 17 [38%] and 15 [33%], respectively, in VRC 320). For VRC5283, 14 of 14 (100%) participants who received split-dose vaccinations by needle-free injection had detectable positive antibody responses, and the geometric mean titre of 304 was the highest across all groups in both trials. INTERPRETATION: VRC5283 was well tolerated and has advanced to phase 2 efficacy testing. FUNDING: Intramural Research Program of the Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health.
Modjarrad, K., L. Lin, S. L. George, K. E. Stephenson, K. H. Eckels, R. A. De La Barrera, R. G. Jarman, E. Sondergaard, J. Tennant, J. L. Ansel, K. Mills, M. Koren, M. L. Robb, J. Barrett, J. Thompson, A. E. Kosel, P. Dawson, A. Hale, C. S. Tan, S. R. Walsh, K. E. Meyer, J. Brien, T. A. Crowell, A. Blazevic, K. Mosby, R. A. Larocca, P. Abbink, M. Boyd, C. A. Bricault, M. S. Seaman, A. Basil, M. Walsh, V. Tonwe, D. F. Hoft, S. J. Thomas, D. H. Barouch and N. L. Michael (2017). “Preliminary aggregate safety and immunogenicity results from three trials of a purified inactivated Zika virus vaccine candidate: phase 1, randomised, double-blind, placebo-controlled clinical trials.” Lancet.
BACKGROUND: A safe, effective, and rapidly scalable vaccine against Zika virus infection is needed. We developed a purified formalin-inactivated Zika virus vaccine (ZPIV) candidate that showed protection in mice and non-human primates against viraemia after Zika virus challenge. Here we present the preliminary results in human beings. METHODS: We did three phase 1, placebo-controlled, double-blind trials of ZPIV with aluminium hydroxide adjuvant. In all three studies, healthy adults were randomly assigned by a computer-generated list to receive 5 mug ZPIV or saline placebo, in a ratio of 4:1 at Walter Reed Army Institute of Research, Silver Spring, MD, USA, or of 5:1 at Saint Louis University, Saint Louis, MO, USA, and Beth Israel Deaconess Medical Center, Boston, MA, USA. Vaccinations were given intramuscularly on days 1 and 29. The primary objective was safety and immunogenicity of the ZPIV candidate. We recorded adverse events and Zika virus envelope microneutralisation titres up to day 57. These trials are registered at ClinicalTrials.gov, numbers NCT02963909, NCT02952833, and NCT02937233. FINDINGS: We enrolled 68 participants between Nov 7, 2016, and Jan 25, 2017. One was excluded and 67 participants received two injections of Zika vaccine (n=55) or placebo (n=12). The vaccine caused only mild to moderate adverse events. The most frequent local effects were pain (n=40 [60%]) or tenderness (n=32 [47%]) at the injection site, and the most frequent systemic reactogenic events were fatigue (29 [43%]), headache (26 [39%]), and malaise (15 [22%]). By day 57, 52 (92%) of vaccine recipients had seroconverted (microneutralisation titre >/=1:10), with peak geometric mean titres seen at day 43 and exceeding protective thresholds seen in animal studies. INTERPRETATION: The ZPIV candidate was well tolerated and elicited robust neutralising antibody titres in healthy adults. FUNDING: Departments of the Army and Defense and National Institute of Allergy and Infectious Diseases.
HIV- Acute Infection
Crowell, T. A., D. J. Colby, S. Pinyakorn, J. L. K. Fletcher, E. Kroon, A. Schuetz, S. J. Krebs, B. M. Slike, L. Leyre, N. Chomont, L. L. Jagodzinski, I. Sereti, N. S. Utay, R. Dewar, R. Rerknimitr, N. Chomchey, R. Trichavaroj, V. G. Valcour, S. Spudich, N. L. Michael, M. L. Robb, N. Phanuphak, J. Ananworanich and R. S. S. Group (2017). “Acute Retroviral Syndrome is Associated with High Viral Burden, CD4 Depletion, and Immune Activation in Systemic and Tissue Compartments.” Clin Infect Dis.
Background: Many individuals with acute HIV infection (AHI) experience acute retroviral syndrome (ARS), which is associated with adverse long-term clinical outcomes. We characterized clinical, virologic, and immunologic features of ARS and described the impact of early antiretroviral therapy (ART) initiation. Methods: Participants presenting for voluntary HIV testing were enrolled during AHI in Bangkok, Thailand. ARS was defined by >/=3 qualifying signs/symptoms. HIV burden, immunophenotypes, and biomarkers were stratified by ARS diagnosis at enrollment and after up to 96 weeks of ART. Results: From 212,382 samples screened, 430 participants were enrolled during AHI, including 335 (78%) with ARS. Median age was 26 years and 416 (97%) were men. Sixty (14%) underwent sigmoid biopsy and 105 (24%) underwent lumbar puncture during AHI. Common symptoms included fever (93%), fatigue (79%), pharyngitis (67%) and headache (64%). Compared to those without ARS, participants with ARS were in later Fiebig stages with higher HIV RNA in blood, colon, and cerebrospinal fluid; higher total HIV DNA in blood; CD4 depletion in blood and colon; and elevated plasma TNFalpha, C-reactive protein, and D-dimer (all p-values <0.05). Subgroup analyses of Fiebig I/II participants (95 with ARS, 69 without) demonstrated similar findings. After 96 weeks of ART, TNFalpha and IL-6 were elevated in the ARS group (p-values <0.05) but other biomarkers equilibrated. Conclusions: ARS was associated with high viral burden, CD4 depletion and immune activation across multiple body compartments during AHI and prior to ART. Persistent inflammation despite suppressive ART could contribute to increased morbidity in individuals who experience ARS.
HIV – Cures & Treatments
Deeks, S. G., S. R. Lewin and L. G. Bekker (2017). “The end of HIV: Still a very long way to go, but progress continues.” PLoS Med 14(11): e1002466.
In an Editorial accompanying PLOS Medicine’s Special Issue on Advances in Prevention, Treatment and Cure of HIV/AIDS, Guest Editors Steven Deeks, Sharon Lewin, and Linda-Gail Bekker discuss priorities in the field and the content of the issue.
Kuo, H. H. and M. Lichterfeld (2017). “Recent progress in understanding HIV reservoirs.” Curr Opin HIV AIDS.
PURPOSE OF REVIEW: Reservoirs of HIV-1-infected cells persist long-term despite highly effective antiretroviral suppression therapy and represent the main barrier against a cure for HIV-1. This review summarizes recent advances in understanding the complexity and diversity of viral reservoir cells. RECENT FINDINGS: Latently infected memory CD4 T cells are the predominant cell compartment responsible for viral persistence, but some studies suggest that myeloid cells, and possibly hematopoietic progenitors, can also serve as long-term viral reservoirs. Specific phenotypic markers, including T-cell activation and exhaustion molecules, may denote CD4 T cells enriched for replication-competent proviruses. Clonal proliferation of infected CD4 T cells in vivo represents an important mechanism responsible for the remarkable long-term stability of the viral reservoir. Multiple new assays, including near full-genome proviral sequencing and simplified versions of viral outgrowth assays, are being developed to analyze and quantify persisting reservoirs of HIV-1-infected cells. SUMMARY: Recent technological advances allow to profile the molecular structure and composition of viral reservoir cells in great detail. Continuous progress in understanding phenotypic and functional properties of viral reservoir cells provides clues for novel clinical interventions to destabilize viral persistence during antiretroviral therapy.
Marques, E. T. A. and D. S. Burke (2017). “Tradition and innovation in development of a Zika vaccine.” Lancet.
Ranganath, N., T. S. Sandstrom, S. C. Burke Schinkel, S. C. Cote and J. B. Angel (2017). “The oncolytic virus, MG1, targets and eliminates latently HIV-1-infected cells: implications for an HIV cure.” J Infect Dis.
Latently HIV-infected cells evade immune- and drug-mediated clearance. These cells harbour intracellular signalling defects including impairment of the antiviral, type I IFN (IFN-I) response. Such defects have also been observed in several cancers, and have been exploited for the development of therapeutic oncolytic viruses, including the recombinant Maraba virus (MG1). We therefore hypothesized that MG1 would infect and eliminate latently HIV-1-infected cells, while sparing healthy uninfected cells. Preferential infection and elimination by MG1 was first demonstrated in latently HIV-1-infected cell lines. Following this, a reduction in HIV-1 DNA and inducible HIV-1 replication was observed following MG1 infection of latently infected, resting CD4 + T-cells generated using an in vitro model of latency. Lastly, MG1 infection resulted in a reduction in HIV-1 DNA and inducible HIV-1 replication in memory CD4+ T-cells isolated from effectively treated, HIV-1-infected individuals. Our results therefore highlight a novel approach to eliminate the latent HIV-1 reservoir.
Dube, K., L. Sylla, L. Dee, J. Taylor, D. Evans, C. D. Bruton, A. Gilberston, L. Gralinski, B. Brown, A. Skinner, B. J. Weiner, S. B. Greene, A. Corneli, A. A. Adimora, J. D. Tucker and S. Rennie (2017). “Research on HIV cure: Mapping the ethics landscape.” PLoS Med 14(12): e1002470.
In an essay, Karine Dube and coauthors discuss the ethics of preclinical and clinical studies relevant to achieving an HIV cure.
HIV- Elite Controllers and Exposed Seronegative
Pernas, M., L. Tarancon-Diez, E. Rodriguez-Gallego, J. Gomez, J. G. Prado, C. Casado, B. Dominguez-Molina, I. Olivares, M. Coiras, A. Leon, C. Rodriguez, J. M. Benito, N. Rallon, M. Plana, O. Martinez-Madrid, M. Dapena, J. A. Iribarren, J. Del Romero, F. Garcia, J. Alcami, M. A. Munoz-Fernandez, F. Vidal, M. Leal, C. Lopez-Galindez and E. Ruiz-Mateos (2017). “Factors Leading to the Loss of Natural Elite Control of HIV-1 Infection.” J Virol.
HIV-1 elite controllers (EC) maintain undetectable viral load (VL) in the absence of antiretroviral treatment. However, these subjects have heterogeneous clinical outcomes including a proportion loosing HIV-1 control over time. In this work we compared, in a longitudinal design, transient EC, analyzed before and after the loss of virological control, versus persistent EC. The aim was to identify factors leading to the loss of natural virological control of HIV-1-infection with a longitudinal retrospective study design. Gag-specific T-cell response was assessed by in vitro intracellular poly-cytokine production quantified by flow cytometry. Viral diversity and sequence-dating were performed in proviral DNA by PCR amplification at limiting dilution in env and gag genes. The expression profile of 70 serum cytokines and chemokines was assessed by multiplex immunoassays. We identified transient EC as subjects with low Gag-specific T-cell polyfunctionality, high viral diversity and high proinflammatory cytokines levels before the loss of control. Gag-specific T-cell polyfunctionality was inversely associated with viral diversity in transient controllers before the loss of control (r=-0.8; p=0.02). RANTES was a potential biomarker of transient control. This study identified, virological and immunological factors including inflammatory biomarkers associated with two different phenotypes within EC. These results may allow a more accurate definition of EC, which could help in a better clinical management of these individuals and in the development of future curative approaches.IMPORTANCE There is a rare group of HIV-infected patients who have the extraordinary capacity to maintain undetectable viral load levels in the absence of antiretroviral treatment, the so called HIV-1 elite controllers (EC). However, there is a proportion within these subjects that eventually loses this capability. In this work we found differences in virological and immune factors including soluble inflammatory biomarkers between subjects with persistent control of viral replication and EC that will loss the virological control. The identification of these factors could be a key point for a right medical care of those EC who are going to lose the natural control of viral replication, and for the design of future immunotherapeutic strategies using as a model the natural persistent control of HIV-infection.
HIV – Evolution
Sato, K., N. Misawa, J. S. Takeuchi, T. Kobayashi, T. Izumi, H. Aso, S. Nagaoka, K. Yamamoto, I. Kimura, Y. Konno, Y. Nakano and Y. Koyanagi (2017). “Experimental adaptive evolution of SIVcpz to pandemic HIV-1 using a humanized mouse model.” J Virol.
HIV-1, the causative agent of AIDS, is originated from SIVcpz, the chimpanzee precursor of the human virus, approximately 100 years ago. This indicates that HIV-1 has emerged through the cross-species transmission of SIVcpz from chimpanzees to humans. However, it remains unclear how SIVcpz has evolved into pandemic HIV-1 in humans. To address this question, we inoculated three SIVcpz (MB897, EK505, and MT145), four pandemic HIV-1 (NL4-3, NLCSFV3, JRCSF and AD8) and 2 non-pandemic HIV-1 (YBF30 and DJO0131) strains. Humanized mice infected with SIVcpz strain MB897, a virus phylogenetically similar to pandemic HIV-1, exhibited a comparable peak viral load to that of mice infected with pandemic HIV-1, while peak viral loads of mice infected with SIVcpz strains EK505 or MT145 as well as non-pandemic HIV-1 strains were significantly lower. These results suggest that SIVcpz strain MB897 is pre-adapted to humans when compared to the other SIVcpz strains. Moreover, viral RNA sequencing of MB897-infected humanized mice identified a nonsynonymous mutation in env, G413R substitution in gp120. The infectivity of the gp120 G413R mutant of MB897 was significantly higher than that of parental MB897. Furthermore, we demonstrated that the gp120 G413R mutant of MB897 augments the capacity for viral replication in both in vitro cell cultures and humanized mice. Taken together, this is the first experimental investigation to use an animal model to demonstrate a gain-of-function evolution of SIVcpz into pandemic HIV-1.ImportanceFrom the mid-20th century, humans are exposed to the menace of viral infectious diseases such as SARS coronavirus, Ebola virus and Zika virus. These outbreaks of emerging/re-emerging viruses can be triggered by cross-species viral transmission from wild animals to humans or zoonoses. HIV-1, the causative agent of AIDS, was emerged by the cross-species transmission of SIVcpz, the HIV-1 precursor in chimpanzee, around 100 years ago. However, the process by which SIVcpz evolved to become HIV-1 in humans remains unclear. By using a hematopoietic stem cell-transplanted humanized mouse model, here we experimentally recapitulate the evolutionary process of SIVcpz to become HIV-1. We provide evidence suggesting that a strain of SIVcpz, MB897, has pre-adapted to infect humans comparing to other SIVcpz strains. We further demonstrate a gain-of-function evolution of SIVcpz in infected humanized mice. Our study reveals that pandemic HIV-1 has emerged through at least two steps: preadaptation and subsequent gain-of-function mutations.
HIV – Models
Moysi, E., K. Padhan, G. Fabozzi and C. Petrovas (2017). “Novel advances on tissue immune dynamics in HIV/simian immunodeficiency virus: lessons from imaging studies.” Curr Opin HIV AIDS.
PURPOSE OF REVIEW: To describe recent findings on the effect of HIV/SIV infection on lymph node viral and T-cell dynamics using imaging-based methodologies. RECENT FINDINGS: Chronic infection, particularly HIV/SIV, alters dramatically the microenvironment, immune cell frequency, distribution, function and tissue organization of secondary lymphoid tissues. These changes are not always reversible. Over the past few years, the implementation of advanced imaging protocols on human lymph node biopsies as well as on longitudinal lymphoid tissues samples from nonhuman primates (NHP) have provided a wealth of information on how local immune responses evolve over time in response to a persisting retroviral pathogen. Most of the information concerns cytotoxic and helper T cells and viral dynamics. In this review, we detail this information focusing on HIV/SIV infection. We also comment on the gaps that imaging technologies have bridged in our understanding and discuss the translational value of these new findings in the light of emerging therapeutic agendas. SUMMARY: Novel imaging platforms allow for dissecting the spatiotemporal dynamics of immune interactions further improving our understanding of the interplay between virus and host and providing important information for designing successful preventive and curative strategies.
Veazey, R. S. and A. A. Lackner (2017). “Nonhuman Primate Models and Understanding the Pathogenesis of HIV Infection and AIDS.” Ilar j.
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals. Research in NHP has led to “dogma changing” discoveries in immunology, infectious disease, and even our own genetics. We now know that many of our genes are retroviral remnants, or developed in response to archaic HIV-like retroviral infections. Early studies involving blood from HIV patients and in experiments in cultured tissues contributed to confusion regarding the cause of AIDS and impeded progress in the development of effective interventions. Research on the many retroviruses of different NHP species have broadened our understanding of human immunology and perhaps even our origins and evolution as a species. In combination with recent advances in molecular biology and computational analytics, research in NHPs has unique potential for discoveries that will directly lead to new cures for old human and animal diseases, including HIV/AIDS.
HIV – Neutralizing Antibodies
Hua, C. K. and M. E. Ackerman (2017). “Increasing the Clinical Potential and Applications of Anti-HIV Antibodies.” Front Immunol 8: 1655.
Preclinical and early human clinical studies of broadly neutralizing antibodies (bNAbs) to prevent and treat HIV infection support the clinical utility and potential of bNAbs for prevention, postexposure prophylaxis, and treatment of acute and chronic infection. Observed and potential limitations of bNAbs from these recent studies include the selection of resistant viral populations, immunogenicity resulting in the development of antidrug (Ab) responses, and the potentially toxic elimination of reservoir cells in regeneration-limited tissues. Here, we review opportunities to improve the clinical utility of HIV Abs to address these challenges and further accomplish functional targets for anti-HIV Ab therapy at various stages of exposure/infection. Before exposure, bNAbs’ ability to serve as prophylaxis by neutralization may be improved by increasing serum half-life to necessitate less frequent administration, delivering genes for durable in vivo expression, and targeting bNAbs to sites of exposure. After exposure and/or in the setting of acute infection, bNAb use to prevent/reduce viral reservoir establishment and spread may be enhanced by increasing the potency with which autologous adaptive immune responses are stimulated, clearing acutely infected cells, and preventing cell-cell transmission of virus. In the setting of chronic infection, bNAbs may better mediate viral remission or “cure” in combination with antiretroviral therapy and/or latency reversing agents, by targeting additional markers of tissue reservoirs or infected cell types, or by serving as targeting moieties in engineered cell therapy. While the clinical use of HIV Abs has never been closer, remaining studies to precisely define, model, and understand the complex roles and dynamics of HIV Abs and viral evolution in the context of the human immune system and anatomical compartmentalization will be critical to both optimize their clinical use in combination with existing agents and define further strategies with which to enhance their clinical safety and efficacy.
Akondy, R. S., M. Fitch, S. Edupuganti, S. Yang, H. T. Kissick, K. W. Li, B. A. Youngblood, H. A. Abdelsamed, D. J. McGuire, K. W. Cohen, G. Alexe, S. Nagar, M. M. McCausland, S. Gupta, P. Tata, W. N. Haining, M. J. McElrath, D. Zhang, B. Hu, W. J. Greenleaf, J. J. Goronzy, M. J. Mulligan, M. Hellerstein and R. Ahmed (2017). “Origin and differentiation of human memory CD8 T cells after vaccination.” Nature.
The differentiation of human memory CD8 T cells is not well understood. Here we address this issue using the live yellow fever virus (YFV) vaccine, which induces long-term immunity in humans. We used in vivo deuterium labelling to mark CD8 T cells that proliferated in response to the virus and then assessed cellular turnover and longevity by quantifying deuterium dilution kinetics in YFV-specific CD8 T cells using mass spectrometry. This longitudinal analysis showed that the memory pool originates from CD8 T cells that divided extensively during the first two weeks after infection and is maintained by quiescent cells that divide less than once every year (doubling time of over 450 days). Although these long-lived YFV-specific memory CD8 T cells did not express effector molecules, their epigenetic landscape resembled that of effector CD8 T cells. This open chromatin profile at effector genes was maintained in memory CD8 T cells isolated even a decade after vaccination, indicating that these cells retain an epigenetic fingerprint of their effector history and remain poised to respond rapidly upon re-exposure to the pathogen.
Chowell, D., L. G. T. Morris, C. M. Grigg, J. K. Weber, R. M. Samstein, V. Makarov, F. Kuo, S. M. Kendall, D. Requena, N. Riaz, B. Greenbaum, J. Carroll, E. Garon, D. M. Hyman, A. Zehir, D. Solit, M. Berger, R. Zhou, N. A. Rizvi and T. A. Chan (2017). “Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy.”Science.
CD8(+) T cell-dependent killing of cancer cells requires efficient presentation of tumor antigens by human leukocyte antigen class I (HLA-I) molecules. However, the extent to which patient-specific HLA-I genotype influences response to anti-PD-1 or anti-CTLA-4 is currently unknown. We determined the HLA-I genotype of 1,535 advanced cancer patients treated with immune checkpoint blockade (ICB). Maximal heterozygosity at HLA-I loci (A, B, and C) improved overall survival after ICB compared to patients who were homozygous for at least one HLA locus. In two independent melanoma cohorts, patients with the HLA-B44 supertype had extended survival, whereas the HLA-B62 supertype (including HLA-B*15:01) or somatic loss of heterozygosity at HLA-I, was associated with poor outcome. Molecular dynamics simulations of HLA-B*15:01 revealed unique elements that may impair CD8(+) T cell recognition of neoantigens. Our results have important implications for predicting response to ICB and for the design of neoantigen-based therapeutic vaccines.
Mennens, S. F. B., M. Bolomini-Vittori, J. Weiden, B. Joosten, A. Cambi and K. van den Dries (2017). “Substrate stiffness influences phenotype and function of human antigen-presenting dendritic cells.” Sci Rep 7(1): 17511.
Dendritic cells (DCs) are specialized immune cells that scan peripheral tissues for foreign material or aberrant cells and, upon recognition of such danger signals, travel to lymph nodes to activate T cells and evoke an immune response. For this, DCs travel large distances through the body, encountering a variety of microenvironments with different mechanical properties such as tissue stiffness. While immune-related pathological conditions such as fibrosis or cancer are associated with tissue stiffening, the role of tissue stiffness in regulating key functions of DCs has not been studied yet. Here, we investigated the effect of substrate stiffness on the phenotype and function of DCs by conditioning DCs on polyacrylamide substrates of 2, 12 and 50 kPa. Interestingly, we found that C-type lectin expression on immature DCs (iDCs) is regulated by substrate stiffness, resulting in differential antigen internalization. Furthermore, we show that substrate stiffness affects beta2 integrin expression and podosome formation by iDCs. Finally, we demonstrate that substrate stiffness influences CD83 and CCR7 expression on mature DCs, the latter leading to altered chemokine-directed migration. Together, our results indicate that DC phenotype and function are affected by substrate stiffness, suggesting that tissue stiffness is an important determinant for modulating immune responses.
Youngblood, B., J. S. Hale, H. T. Kissick, E. Ahn, X. Xu, A. Wieland, K. Araki, E. E. West, H. E. Ghoneim, Y. Fan, P. Dogra, C. W. Davis, B. T. Konieczny, R. Antia, X. Cheng and R. Ahmed (2017). “Effector CD8 T cells dedifferentiate into long-lived memory cells.” Nature.
Memory CD8 T cells that circulate in the blood and are present in lymphoid organs are an essential component of long-lived T cell immunity. These memory CD8 T cells remain poised to rapidly elaborate effector functions upon re-exposure to pathogens, but also have many properties in common with naive cells, including pluripotency and the ability to migrate to the lymph nodes and spleen. Thus, memory cells embody features of both naive and effector cells, fuelling a long-standing debate centred on whether memory T cells develop from effector cells or directly from naive cells. Here we show that long-lived memory CD8 T cells are derived from a subset of effector T cells through a process of dedifferentiation. To assess the developmental origin of memory CD8 T cells, we investigated changes in DNA methylation programming at naive and effector cell-associated genes in virus-specific CD8 T cells during acute lymphocytic choriomeningitis virus infection in mice. Methylation profiling of terminal effector versus memory-precursor CD8 T cell subsets showed that, rather than retaining a naive epigenetic state, the subset of cells that gives rise to memory cells acquired de novo DNA methylation programs at naive-associated genes and became demethylated at the loci of classically defined effector molecules. Conditional deletion of the de novo methyltransferase Dnmt3a at an early stage of effector differentiation resulted in reduced methylation and faster re-expression of naive-associated genes, thereby accelerating the development of memory cells. Longitudinal phenotypic and epigenetic characterization of the memory-precursor effector subset of virus-specific CD8 T cells transferred into antigen-free mice revealed that differentiation to memory cells was coupled to erasure of de novo methylation programs and re-expression of naive-associated genes. Thus, epigenetic repression of naive-associated genes in effector CD8 T cells can be reversed in cells that develop into long-lived memory CD8 T cells while key effector genes remain demethylated, demonstrating that memory T cells arise from a subset of fate-permissive effector T cells.
Vaccine Design Immunogenicity Efficacy
Hegde, N. R., S. Gauthami, H. M. Sampath Kumar and J. Bayry (2017). “The use of databases, data mining and immunoinformatics in vaccinology: where are we?” Expert Opin Drug Discov: 1-14.
INTRODUCTION: Vaccinology has evolved from a sub-discipline focussed on simplistic vaccine development based on antibody-mediated protection to a separate discipline involving epidemiology, host and pathogen biology, immunology, genomics, proteomics, structure biology, protein engineering, chemical biology, and delivery systems. Data mining in combination with bioinformatics has provided a scaffold linking all these disciplines to the design of vaccines and vaccine adjuvants. Areas covered: This review provides background knowledge on immunological aspects which have been exploited with informatics for the in silico analysis of immune responses and the design of vaccine antigens. Furthermore, the article presents various databases and bioinformatics tools, and discusses B and T cell epitope predictions, antigen design, adjuvant research and systems immunology, highlighting some important examples, and challenges for the future. Expert opinion: Informatics and data mining have not only reduced the time required for experimental immunology, but also contributed to the identification and design of novel vaccine candidates and the determination of biomarkers and pathways of vaccine response. However, more experimental data is required for benchmarking immunoinformatic tools. Nevertheless, developments in immunoinformatics and reverse vaccinology, which are nascent fields, are likely to hasten vaccine discovery, although the path to regulatory approval is likely to remain a necessary impediment
Kim, K. W., S. Jeong, K. B. Ahn, J. S. Yang, C. H. Yun and S. H. Han (2017). “Guinea pig complement potently measures vibriocidal activity of human antibodies in response to cholera vaccines.” J Microbiol 55(12): 973-978.
The vibriocidal assay using guinea pig complement is widely used for the evaluation of immune responses to cholera vaccines in human clinical trials. However, it is unclear why guinea pig complement has been used over human complement in the measurement of vibriocidal activity of human sera and there have not been comparison studies for the use of guinea pig complement over those from other species. Therefore, we comparatively investigated the effects of complements derived from human, guinea pig, rabbit, and sheep on vibriocidal activity. Complements from guinea pig, rabbit, and human showed concentration-dependent vibriocidal activity in the presence of quality control serum antibodies. Of these complements, guinea pig complement was the most sensitive and effective over a wide concentration range. When the vibriocidal activity of complements was measured in the absence of serum antibodies, human, sheep, and guinea pig complements showed vibriocidal activity up to 40-fold, 20-fold, and 1-fold dilution, respectively. For human pre- and post-vaccination sera, the most potent vibriocidal activity was observed when guinea pig complement was used. In addition, the highest fold-increases between pre- and post- vaccinated sera were obtained with guinea pig complement. Furthermore, human complement contained a higher amount of V. cholerae- and its lipopolysaccharide-specific antibodies than guinea pig complement. Collectively, these results suggest that guinea pig complements are suitable for vibriocidal assays due to their high sensitivity and effectiveness to human sera.
Komarova, T. R. V., E. V. Sheshukova and Y. L. Dorokhov (2017). “Plant-Made Antibodies: Properties and Therapeutic Applications.” Curr Med Chem.
A cost-effective plant platform for therapeutic monoclonal antibody production is both flexible and scalable. In addition, plant-made antibodies (PMAbs) could be advantageous compared to those produced in animal cells due to the absence of a risk of contamination from nucleic acids or proteins of animal origin. In this review, the various platforms of PMAbs production are described, and the widely used transient expression system based on Agrobacterium-mediated delivery of genetic material into plant cells is discussed in detail. Plants produce less complex and diverse Asn-attached glycans compared to animal cells and contain plant-specific residues. In this review, we examine the features of and approaches to humanizing the Asn297-linked glycan of PMAbs. The prospects for PMAbs in the prevention and treatment of human infectious diseases have been illustrated by promising results with PMAbs against Human immunodeficiency virus, rotavirus infection, Human respiratory syncytial virus, rabies, anthrax and Ebola virus. The pre-clinical and clinical trials of PMAbs against different types of cancer, including lymphoma and breast cancer, are addressed.
Stitz, L., A. Vogel, M. Schnee, D. Voss, S. Rauch, T. Mutzke, T. Ketterer, T. Kramps and B. Petsch (2017). “A thermostable messenger RNA based vaccine against rabies.” PLoS Negl Trop Dis 11(12): e0006108.
Although effective rabies virus vaccines have been existing for decades, each year, rabies virus infections still cause around 50.000 fatalities worldwide. Most of these cases occur in developing countries, where these vaccines are not available. The reasons for this are the prohibitive high costs of cell culture or egg grown rabies virus vaccines and the lack of a functional cold chain in many regions in which rabies virus is endemic. Here, we describe the excellent temperature resistance of a non-replicating mRNA based rabies virus vaccine encoding the rabies virus glycoprotein (RABV-G). Prolonged storage of the vaccine from -80 degrees C to up to +70 degrees C for several months did not impact the protective capacity of the mRNA vaccine. Efficacy after storage was demonstrated by the induction of rabies specific virus neutralizing antibodies and protection in mice against lethal rabies infection. Moreover, storing the vaccine at oscillating temperatures between +4 degrees and +56 degrees C for 20 cycles in order to simulate interruptions of the cold chain during vaccine transport, did not affect the vaccine’s immunogenicity and protective characteristics, indicating that maintenance of a cold chain is not essential for this vaccine.