Design Of Therapeutic Vaccines Research Articles

Abstract B055: A pan-HLA HPV16 T cell epitope repertoire – validated by immunopeptidomics and immunogenicity analysis – for therapeutic vaccine design

Abstract B055: A pan-HLA HPV16 T cell epitope repertoire – validated by immunopeptidomics and immunogenicity analysis – for therapeutic vaccine design

Analysis of virulence factors in extracellular vesicles secreted by Naegleria fowleri

Naegleria fowleri is the etiological agent of primary amebic meningoencephalitis (PAM), a rapidly progressive acute and fulminant infection that affects the central nervous system, particularly of children and young adults, which has a mortality rate greater than 95%, and its symptomatologic similarity with other meningitis caused by virus or bacteria makes it difficult to make a quick and timely diagnosis that prevents the progression of the infection. It is necessary to know the antigenic determinants as well as the pathogenicity mechanisms of this amoeba to implement strategies that allow for better antiamoebic therapeutic and diagnostic targets that directly impact the health sector. Therefore, the aim of this work was to analyze some virulence factors as part of extracellular vesicle (EV) cargo secreted by N. fowleri. The EV secretion to the extracellular medium was evaluated in trophozoites fixed and incubated with anti-N. fowleri antibody while molecular identification of EV cargo was performed by SDS-PAGE, Western blot, and RT-PCR. Our results showed that N. fowleri secretes a wide variety of vesicle sizes ranging from 0.2 to > 2 μm, and these EVs were recognized by antibodies anti-Naegleropore B, anti-19 kDa polypeptide band, anti-membrane protein Mp2CL5, anti-protease cathepsin B, and anti-actin. Furthermore, these vesicles were localized in the trophozoites cytoplasm or secreted into the extracellular medium. Specifically in relation to small vesicles, our purified exosomes were recognized by CD63 and Hsp70 markers, along with the previously mentioned proteins. RT-PCR analysis was made through the isolation of EVs from N. fowleri trophozoite culture by concentration, filtration, and ultracentrifugation. Interestingly, we obtained PCR products for Nfa1, NPB, Mp2CL5, and CatB genes as part of exosomes cargo. This suggests that the molecules identified in this work could play an important role in communication as well as in infectious processes caused by this amoeba. Therefore, the study and characterization of the pathogenicity mechanisms, as well as the virulence factors released by N. fowleri remains a key point to provide valuable information for the development of therapeutic treatments, vaccine design, or biomarkers for a timely diagnosis against infections caused by protozoa.

IL-15 Complex-Induced IL-10 Enhances Plasmodium-specific CD4+ T Follicular Helper Differentiation and Antibody Production.

Malaria, which results from infection with Plasmodium parasites, remains a major public health problem. Although humans do not develop long-lived, sterilizing immunity, protection against symptomatic disease develops after repeated exposure to Plasmodium parasites and correlates with the acquisition of humoral immunity. Despite the established role Abs play in protection from malaria disease, dysregulated inflammation is thought to contribute to the suboptimal immune response to Plasmodium infection. Plasmodium berghei ANKA (PbA) infection results in a fatal severe malaria disease in mice. We previously demonstrated that treatment of mice with IL-15 complex (IL-15C; IL-15 bound to an IL-15Rα-Fc fusion protein) induces IL-10 expression in NK cells, which protects mice from PbA-induced death. Using a novel MHC class II tetramer to identify PbA-specific CD4+ T cells, in this study we demonstrate that IL-15C treatment enhances T follicular helper (Tfh) differentiation and modulates cytokine production by CD4+ T cells. Moreover, genetic deletion of NK cell-derived IL-10 or IL-10R expression on T cells prevents IL-15C-induced Tfh differentiation. Additionally, IL-15C treatment results in increased anti-PbA IgG Ab levels and improves survival following reinfection. Overall, these data demonstrate that IL-15C treatment, via its induction of IL-10 from NK cells, modulates the dysregulated inflammation during Plasmodium infection to promote Tfh differentiation and Ab generation, correlating with improved survival from reinfection. These findings will facilitate improved control of malaria infection and protection from disease by informing therapeutic strategies and vaccine design.

Cancer vaccines: from an immunology perspective.

The concept of a therapeutic cancer vaccine to activate anti-tumour immunity pre-dates innovations in checkpoint blockade immunotherapies. However, vaccination strategies have yet to show the hoped-for successes in patients, and unanswered questions regarding the underlying immunological mechanisms behind cancer vaccines have hampered translation to clinical practice. Recent advances in our understanding of the potential of tumour mutational burden and neo-antigen-reactive T cells for response to immunotherapy have re-ignited enthusiasm for cancer vaccination strategies, coupled with the development of novel mRNA-based vaccines following successes in prevention of COVID-19. Here we summarise current developments in cancer vaccines and discuss how advances in our comprehension of the cellular interplay in immunotherapy-responsive tumours may inform better design of therapeutic cancer vaccines, with a focus on the role of dendritic cells as the orchestrators of anti-tumour immunity. The increasing number of clinical trials and research being funnelled into cancer vaccines has demonstrated the 'proof-of-principle', supporting the hypothesis that therapeutic vaccines have potential as an immuno-oncology agent. For efficacious and safe cancer vaccines to be developed, better understanding of the underpinning immunological mechanisms is paramount.

Induction of broad multifunctional CD8+ and CD4+ T cells by hepatitis B virus antigen-based synthetic long peptides ex vivo.

Therapeutic vaccination based on synthetic long peptides (SLP®) containing both CD4+ and CD8+ T cell epitopes is a promising treatment strategy for chronic hepatitis B infection (cHBV). We designed SLPs for three HBV proteins, HBcAg and the non-secreted proteins polymerase and X, and investigated their ability to induce T cell responses ex vivo. A set of 17 SLPs was constructed based on viral protein conservation, functionality, predicted and validated binders for prevalent human leukocyte antigen (HLA) supertypes, validated HLA I epitopes, and chemical producibility. All 17 SLPs were capable of inducing interferon gamma (IFNɣ) production in samples from four or more donors that had resolved an HBV infection in the past (resolver). Further analysis of the best performing SLPs demonstrated activation of both CD8+ and CD4+ multi-functional T cells in one or more resolver and patient sample(s). When investigating which SLP could activate HBV-specific T cells, the responses could be traced back to different peptides for each patient or resolver. This indicates that a large population of subjects with different HLA types can be covered by selecting a suitable mix of SLPs for therapeutic vaccine design. In conclusion, we designed a set of SLPs capable of inducing multifunctional CD8+ and CD4+ T cells ex vivo that create important components for a novel therapeutic vaccine to cure cHBV.

Initial immune response after exposure to Mycobacterium tuberculosis or to SARS-COV-2: similarities and differences.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) and Coronavirus disease-2019 (COVID-19), whose etiologic agent is severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), are currently the two deadliest infectious diseases in humans, which together have caused about more than 11 million deaths worldwide in the past 3 years. TB and COVID-19 share several aspects including the droplet- and aerosol-borne transmissibility, the lungs as primary target, some symptoms, and diagnostic tools. However, these two infectious diseases differ in other aspects as their incubation period, immune cells involved, persistence and the immunopathological response. In this review, we highlight the similarities and differences between TB and COVID-19 focusing on the innate and adaptive immune response induced after the exposure to Mtb and SARS-CoV-2 and the pathological pathways linking the two infections. Moreover, we provide a brief overview of the immune response in case of TB-COVID-19 co-infection highlighting the similarities and differences of each individual infection. A comprehensive understanding of the immune response involved in TB and COVID-19 is of utmost importance for the design of effective therapeutic strategies and vaccines for both diseases.

Immunoinformatics studies of heat shock proteins 27 and 70: Development of potent therapeutic vaccine constructs against human papillomavirus-related cancers

Heat shock proteins (HSPs) improve cross-presentation of linked tumor antigens, thus they can be exploited in therapeutic vaccine design. Herein, in silico analyses of different vaccine constructs were performed based on human papillomavirus (HPV)-16 E7 protein linked to Homo sapiens/Mus musculus Hsp27 or Hsp70 in multiepitope and whole sequence forms. Then, computational comparison between different orientations of Hsp/E7 was carried out in both forms. Finally, molecular docking was performed between the designed constructs and signaling (TLRs) or endocytic (CD14, LOX-1 and SREC-1) receptors. Our data represented the high-ranked T-cell epitopes and the potential B-cell epitopes of Homo sapiens/Mus musculus Hsp27 and Hsp70. Moreover, molecular docking showed that whole sequence of Hsp27 had better interaction with all receptors than whole sequence of Hsp70 suggesting likely stronger stimulation of innate and adaptive immunity. All designed Homo sapiens/Mus musculus Hsp27/E7 constructs had better docking scores with the endocytic receptors especially SREC-1 than all designed Homo sapiens/Mus musculus Hsp70/E7 constructs in both orientations. Generally, the multiepitope-/whole sequence-based Homo sapiens/Mus musculus Hsp27-E7 fusion constructs showed more conservancy and immunogenicity than other designed constructs. These fusion constructs were non-allergenic, non-toxic and stable suggesting them as promising vaccine candidates against HPV-related cancers.

Mannan-decorated STING-activating vaccine carrier for spatial coordinative stimulating antigen-specific immune responses

In recent years, the use of nanotechnologies to improve immunotherapy efficiency has attracted increasing interest in preventive and therapeutic cancer vaccine design. However, current nanocarriers are restricted by difficulties in the systematic spatial coordinative transport of antigens, which greatly hampers the immune response efficacy of nanovaccines. Herein, we designed a mannan-decorated stimulator of the interferon genes (STING)-activating vaccine carrier for spatial coordinative stimulation of antigen-specific immune responses and elicitation of robust antitumor immunity. Mannan-decoration as the shell could significantly enhance the lymph node draining ability of the nanovaccines, especially in CD8+ dendritic cells (DCs). Azole molecule end-capped polylactic acid-polyethylenimine (PLA-PEI-4BImi) with innate stimulating activity was applied as the inner core for coordinating antigen-presenting cell activation and antigen cross-presentation. In the in vivo therapy study, single usage of this nanovaccine could achieve a 93% tumor suppression rate in the B16-OVA tumor model, which is superior to the commercialized aluminum adjuvant. This study demonstrates that a rational design of vaccine carriers for solving spatial transmission issues could greatly improve cancer vaccine efficiencies.

CaCO3 powder-mediated biomineralization of antigen nanosponges synergize with PD-1 blockade to potentiate anti-tumor immunity

Antigen self-assembly nanovaccines advance the minimalist design of therapeutic cancer vaccines, but the issue of inefficient cross-presentation has not yet been fully addressed. Herein, we report a unique approach by combining the concepts of “antigen multi-copy display” and “calcium carbonate (CaCO3) biomineralization” to increase cross-presentation. Based on this strategy, we successfully construct sub-100 nm biomineralized antigen nanosponges (BANSs) with high CaCO3 loading (38.13 wt%) and antigen density (61.87%). BANSs can be effectively uptaken by immature antigen-presenting cells (APCs) in the lymph node upon subcutaneous injection. Achieving efficient spatiotemporal coordination of antigen cross-presentation and immune effects, BANSs induce the production of CD4+ T helper cells and cytotoxic T lymphocytes, resulting in effective tumor growth inhibition. BANSs combined with anti-PD-1 antibodies synergistically enhance anti-tumor immunity and reverse the tumor immunosuppressive microenvironment. Overall, this CaCO3 powder-mediated biomineralization of antigen nanosponges offer a robust and safe strategy for cancer immunotherapy.

MRNA-lipid Nanoparticle Vaccines: Structure and Delivery

As the latest generation of vaccine production technology, mRNA vaccine has achieved vaccine production and clinical application, such as COVID-19 mRNA vaccine. However, a substantial inherent limitation in the development of mRNA vaccines is that mRNA is chemically unstable and susceptible to lysed by lysosome. Therefore, it is necessary to develop suitable vectors for mRNA. Today, the mainly COVID-19 vaccines include mRNA produced by Modera was approved by the FDA in the world. mRNA-1273 is a nucleic acid vaccine delivered by a lipid nanoparticle (LNP). As mRNA vaccines become widely available for mass vaccination, LNP have emerged as a popular delivery system. In this review, we introduce the history of MRNA after starting from mRNA vaccines, discusses the structure of LNP including ionizable cationic lipids, cholesterol, neutral lipids, PEG-lipids, and the role of each component. It also explains the mechanism of LNP delivery in mRNA vaccine and introduces different types of LNP, and describes several factors affecting particle delivery. It has been shown that the delivery of LNP is affected by particle size, particle surface charge, surface polyethylene glocalization and specific targeting modification. This review serves as a useful provides for insights into the delivery of LNP and the design of new therapeutic vaccines.

Activation of CD4 T cells during prime immunization determines the success of a therapeutic hepatitis B vaccine in HBV-carrier mouse models

We recently developed a heterologous therapeutic vaccination scheme (TherVacB) comprising a particulate protein prime followed by a modified vaccinia-virus Ankara (MVA)-vector boost for the treatment of HBV. However, the key determinants required to overcome HBV-specific immune tolerance remain unclear. Herein, we aimed to study new combination adjuvants and unravel factors that are essential for the antiviral efficacy of TherVacB. Recombinant hepatitis B surface and core antigen (HBsAg and HBcAg) particles were formulated with different liposome- or oil-in-water emulsion-based combination adjuvants containing saponin QS21 and monophosphoryl lipid A; these formulations were compared to STING-agonist c-di-AMP and conventional aluminium hydroxide formulations. Immunogenicity and the antiviral effects of protein antigen formulations and the MVA-vector boost within TherVacB were evaluated in adeno-associated virus-HBV-infected and HBV-transgenic mice. Combination adjuvant formulations preserved HBsAg and HBcAg integrity for ≥12 weeks, promoted human and mouse dendritic cell activation and, within TherVacB, elicited robust HBV-specific antibody and T-cell responses in wild-type and HBV-carrier mice. Combination adjuvants that prime a balanced HBV-specific type 1 and 2T helper response induced high-titer anti-HBs antibodies, cytotoxic T-cell responses and long-term control of HBV. In the absence of an MVA-vector boost or following selective CD8 T-cell depletion, HBsAg still declined (mediated mainly by anti-HBs antibodies) but HBV replication was not controlled. Selective CD4 T-cell depletion during the priming phase of TherVacB resulted in a complete loss of vaccine-induced immune responses and its therapeutic antiviral effect in mice. Our results identify CD4 T-cell activation during the priming phase of TherVacB as a key determinant of HBV-specific antibody and CD8 T-cell responses. Therapeutic vaccination is a potentially curative treatment option for chronic hepatitis B. However, it remains unclear which factors are essential for breaking immune tolerance in HBV carriers and determining successful outcomes. Our study provides the first direct evidence that efficient priming of HBV-specific CD4 T cells determines the success of therapeutic hepatitis B vaccination in two preclinical HBV-carrier mouse models. Applying an optimal formulation of HBV antigens that activates CD4 and CD8 T cells during prime immunization provided the foundation for an antiviral effect of therapeutic vaccination, while depletion of CD4 T cells led to a complete loss of vaccine-induced antiviral efficacy. Boosting CD8 T cells was important to finally control HBV in these mouse models. Our findings provide important insights into the rational design of therapeutic vaccines for the cure of chronic hepatitis B.

Studying antigen presentation in chronic hepatitis B infection and liver cancer for therapeutic vaccine design

Worldwide about 250 million people are affected by chronic HBV infection (CHB). CHB patients are prone to develop cirrhosis and liver cancer, leading to approximately 1 million deaths each year. Currently, no effective treatment for CHB or liver cancer exists. Antigen specific immunotherapy represents an attractive treatment option. To develop such therapy insight into the presentation of viral and/or tumor antigens in CHB and liver cancer is required. Our efforts to identify target antigens & epitopes for immunotherapy and the subsequent translation of this knowledge towards clinical application will be discussed.

Rational Design of T-Cell- and B-Cell-Based Therapeutic Cancer Vaccines.

Cancer vaccines provide an efficient strategy to enhance tumor-specific immune responses by redeploying immune systems. Despite the approval of the first cancer vaccine (Sipuleucel-T) by the U.S. Food and Drug Administration in 2010, most therapeutic cancer vaccines fail in clinical trials. Basically, tumor-specific immune responses rely on not only T-cell but also B-cell immunity, which indicates that cancer vaccines should leverage both arms of the adaptive immune system. For example, CD8+ T cells activated by antigen-presenting cells (APCs) recognize and directly kill tumor cells via peptide-bound major histocompatibility complex (pMHC). B cells recognize antigen with no need of pMHC and require CD4+ T cells for sufficient activation and antibody generation, enabling antibody-mediated nondirect killing on tumor cells. Considering the different mechanisms of T-cell and B-cell activation, the rational design of therapeutic cancer vaccines should consider several factors, including antigen selection and recognition, immune activation, vaccine delivery, and repeatable vaccination, which can be advanced by chemical strategies.In this Account, we summarize our recent contributions to the development of effective T-cell- and B-cell-based therapeutic cancer vaccines. For T-cell-based vaccines, we focus on adjuvants as the key component for controllable APC activation and T-cell priming. Not only synthetic molecular agonists of pattern recognition receptors (PRRs) but also adjuvant nanomaterials were explored to satisfy diversiform vaccine designs. For example, a type of natural cyclic dinucleotide (CDN) that was chemically modified with fluorination and ipsilateral phosphorothioation to activate the stimulator of interferon gene (STING) was found to mediate antitumor responses. It retains structural similarity to the parent CDN scaffold but possesses increased stability, cellular uptake, and immune activation for antitumor treatment. It also facilitates facile conjugation with other agonists, which not only enhances APC-targeting delivery but also balances cellular and humoral antitumor responses. We also explored the intrinsic properties of nanomaterials that allow them to serve as adjuvants. A black phosphorus nanosheet-based nanovaccine was constructed and found to strongly potentiate antigen-specific T-cell antitumor immune responses through multiple immune-potentiating properties, leading to a highly integrated nanomaterial-based adjuvant design. For B-cell-based vaccines, multicomponent and multivalent strategies were applied to improve the immunogenicity. A multicomponent linear vaccine conjugate coordinates helper T (Th) cells and APCs to proliferate and differentiates B cells for enhanced antitumor immunoglobulin G antibody responses. To further improve antigen recognition, clustered designs on a multivalent epitope were applied by generating various structures, including branched lysine-based peptides, natural multivalent scaffold molecules, and self-assembled nanofibers. We also engineered nano- and microvaccine systems to optimize systemic and localized vaccination. A multilayer-assembled nanovaccine successfully integrated antigens and multiple agonists to modulate APC activation. A DNA hydrogel contributed to the control of APC's immune behaviors, including cell recruitment, activation, and migration, and induced robust antitumor responses as an all-in-one designable platform. In this Account, by summarizing strategies for both T-cell- and B-cell-based vaccine design, we not only compare the differences but also address the intrinsic uniformity between such vaccine designs and further discuss the potential of a combined T-cell- and B-cell-based vaccine, which highlights the applicability and feasibility of chemical strategies.

A Highly Effective System for Predicting MHC-II Epitopes With Immunogenicity.

In the past decade, the substantial achievements of therapeutic cancer vaccines have shed a new light on cancer immunotherapy. The major challenge for designing potent therapeutic cancer vaccines is to identify neoantigens capable of inducing sufficient immune responses, especially involving major histocompatibility complex (MHC)-II epitopes. However, most previous studies on T-cell epitopes were focused on either ligand binding or antigen presentation by MHC rather than the immunogenicity of T-cell epitopes. In order to better facilitate a therapeutic vaccine design, in this study, we propose a revolutionary new tool: a convolutional neural network model named FIONA (Flexible Immunogenicity Optimization Neural-network Architecture) trained on IEDB datasets. FIONA could accurately predict the epitopes presented by the given specific MHC-II subtypes, as well as their immunogenicity. By leveraging the human leukocyte antigen allele hierarchical encoding model together with peptide dense embedding fusion encoding, FIONA (with AUC = 0.94) outperforms several other tools in predicting epitopes presented by MHC-II subtypes in head-to-head comparison; moreover, FIONA has unprecedentedly incorporated the capacity to predict the immunogenicity of epitopes with MHC-II subtype specificity. Therefore, we developed a reliable pipeline to effectively predict CD4+ T-cell immune responses against cancer and infectious diseases.

NK cell-derived IL-10 enhances Plasmodium-specific CD4+ Tfh differentiation and IL-27 production in mice

Abstract Malaria, which results from infection with Plasmodium parasites, remains a major public health problem with over 200 million cases and nearly 500,000 deaths annually. Although long-lived, sterilizing immunity does not develop in humans following repeated exposure to Plasmodium parasites, protection against symptomatic disease correlates with the acquisition of humoral immunity. Despite the established role antibodies play in protection to malaria disease, excessive inflammation is thought to contribute to the ineffective immune response to Plasmodium infection. Plasmodium berghei ANKA (PbA) infection results in a fatal severe malaria disease in mice. We previously showed that treatment of mice with IL-15 complex (IL-15C; IL-15 bound to an IL-15Rα-Fc fusion protein) induces IL-10 expression in NK cells, which protects mice from PbA-induced death by dampening the fatal inflammatory response. Interestingly, IL-15C treatment promotes Tfh differentiation at 7 days post-PbA infection (dpi), and genetic deletion of NK cell-derived IL-10 or antibody blockade of IL-10R prevents IL-15C-induced Tfh differentiation. Additionally, IL-15C treatment enhances CD4 T cell-derived IL-27p28 production at 7 dpi and results in increased anti-PbA IgG antibody levels at 42 dpi. These data suggest that IL-15C treatment, via its induction of IL-10 from NK cells, modulates the inflammatory milieu to promote Tfh differentiation, IL-27 production, and PbA-specific antibody generation. These findings will facilitate improved control of malaria infection and protection from disease by informing therapeutic strategies and vaccine design. Supported by grants from NIH (K22 AI143969-01A1, K08 AI141761-01)

Photosensitizer-induced HPV16 E7 nanovaccines for cervical cancer immunotherapy

There is a lack of effective treatment methods for advanced cervical, and the therapeutic HPV vaccine is a promising option. The design of an efficient therapeutic vaccine is one of the main challenges. In the current study, we constructed a novel HPV nanovaccine that could effectively inhibit the progression of cervical cancer by combining nanotechnology and photodynamic therapy. This nanovaccine was constructed by linking bovine serum albumin (BSA) with the E7 antigen and then encapsulating the photosensitizer and adjuvant through disulfide bonds to form a highly biocompatible and stable structure. Due to its slow-release properties and targeted delivery to lymph nodes combined with infrared laser irradiation of photosensitizers to produce a photo-oxygen response, this vaccine could effectively induce the maturation of dendritic cells and stimulate T cell effects, thereby enhancing antitumor immunity. This prevention and treatment of tumors was experimentally demonstrated in a TC-1 cervical cancer model in C57BL/6 mice. This strategy can be applied to the design of therapeutic HPV vaccines in the future for clinical use.

A Minimalist Binary Vaccine Carrier for Personalized Postoperative Cancer Vaccine Therapy.

In recent years, significant evolutions have been made in applying nanotechnologies for prophylactic and therapeutic cancer vaccine design. However, the clinical translation of nanovaccines is still limited owing to their complicated compositions and difficulties in the spatiotemporal coordination of antigen-presenting cell activation and antigen cross-presentation. Herein, a minimalist binary nanovaccine (BiVax) is designed that integrates innate stimulating activity into the carrier to elicit robust antitumor immunity. The authors started by making a series of azole molecules end-capped polyethylenimine (PEI-M), and weresurprised to find that over 60% of the PEI-M polymers have innate stimulating activity via activation of the stimulator of interferon genes pathway. PEI-4BImi, a PEI-M obtained from a series of polymers, elicits robust antitumor immune responses when used as a subcutaneously injected nanovaccine by simply mixing with ovalbumin antigens, and this BiVax system performs much better than the traditional ternary vaccine system, as well as, commercialized aluminum-containing adjuvants. This system also enables the fast preparation of personalized BiVax by compositing PEI-4BImi with autologous tumor cell membrane protein antigens, and a 60% postoperative cure rate is observed when combined with immune checkpoint inhibitors.

The polymorphism analysis and epitope predicted of Alphapapillomavirus 9 E6 in Sichuan, China

BackgroundThe Alphapapillomavirus 9 (α-9 HPV) is a member of the Alphapapillomavirus genus and Papillomaviridae family. These viruses are almost all carcinogenic HPV, which is closely related to 75% of invasive cervical cancer worldwide, and has a high prevalence in Sichuan. The carcinogenic function is mainly realized by its E6 oncoprotein.MethodsCell samples were collected by cervical scraped for HPV detecting and typing. HPV-16, HPV-31, HPV-33, HPV-52, HPV-58 5 α-9 genus HPV subtype positive samples were selected, their E6 gene was sequenced and analyzed. The positive selection sites of HPV E6 genes were estimated by PAML 4.8 server. The secondary and tertiary structure of E6 protein were predicted by PSIPred and Swiss-model. The T-cell antigen epitopes of E6 protein were predicted by IEDB.Resultsα-9 HPV has a high prevalence in Sichuan, China. From 2012 to 2017, 18,067 cell cervical samples were collected, and 3135 were detected with α-9 HPV infection. Among which, 250 cases HPV-16 E6, 96 cases HPV-31 E6, 216 cases HPV-33 E6, 288 cases HPV-52 E6 and 405 cases HPV-58 E6 were successfully amplified, 17, 6, 6, 13, and 4 non-synonymous nucleotide mutations were respectively detected in HPV-16, 31, 33, 52, and 58 E6, 7 positive selection sites of α-9 HPV E6 were selected out (D32E of HPV-16 E6, K35N, K93N and R145I of HPV-33 E6, K93R of HPV-52 E6, K93N and R145K of HPV-58 E6). The structure and antigen epitopes of E6 protein with amino acid substitution differ from those of wild-type E6 protein, especially for the mutation located in the E6 positive selection site.ConclusionsHPV E6 nucleotide non-synonymous mutation in the positive selection site influence the protein structure and decrease the antigen epitopes affinity of the E6 protein overall, making it more difficult for the HPV-infected cells to be detected by the immune system, and enhancing the HPV adaptability to the environment. Mutations influence the validity of HPV clinical diagnostic probes, the polymorphism analysis of α-9 HPV E6 enrich the data of HR-risk HPV in Sichuan China, and the detection probes designed with the polymorphism data in mind can improve the efficiency of clinical detection; Mutations influence epitopes affinity, the association of E6 polymorphism and epitope affinity can improve the design of therapeutic vaccine with good immunity and high generality antigen epitope; The above study all provide a good theoretical basis for the prevention and treatment of HPV-related diseases.

Beyond Sequencing: Prioritizing and Delivering Neoantigens for Cancer Vaccines.

Neoantigens are tumor-specific proteins and peptides that can be highly immunogenic. Immune-mediated tumor rejection is strongly associated with cytotoxic responses to neoantigen-derived peptides in noncovalent association with self-HLA molecules. Neoantigen-based therapies, such as adoptive T cell transfer, have shown the potential to induce remission of treatment-resistant metastatic disease in select patients. Cancer vaccines are similarly designed to elicit or amplify antigen-specific T cell populations and stimulate directed antitumor immunity, but the selection and prioritization of the neoantigens remains a challenge. Bioinformatic algorithms can predict tumor neoantigens from somatic mutations, insertion-deletions, and other aberrant peptide products, but this often leads to hundreds of potential neoepitopes, all unique for that tumor. Selecting neoantigens for cancer vaccines is complicated by the technical challenges of neoepitope discovery, the diversity of HLA molecules, and intratumoral heterogeneity of passenger mutations leading to immune escape. Despite strong preclinical evidence, few neoantigen cancer vaccines tested in vivo have generated epitope-specific T cell populations, suggesting suboptimal immune system activation. In this chapter, we review factors affecting the prioritization and delivery of candidate neoantigens in the design of therapeutic and preventive cancer vaccines and consider synergism with standard chemotherapies.

A Role for B Cells to Transmit Hepatitis C Virus Infection.

Hepatitis C virus (HCV) is highly variable and transmits through infected blood to establish a chronic liver infection in the majority of patients. Our knowledge on the infectivity of clinical HCV strains is hampered by the lack of in vitro cell culture systems that support efficient viral replication. We and others have reported that HCV can associate with and infect immune cells and may thereby evade host immune surveillance and elimination. To evaluate whether B cells play a role in HCV transmission, we assessed the ability of B cells and sera from recent (<2 years) or chronic (≥ 2 years) HCV patients to infect humanized liver chimeric mice. HCV was transmitted by B cells from chronic infected patients whereas the sera were non-infectious. In contrast, B cells from recently infected patients failed to transmit HCV to the mice, whereas all serum samples were infectious. We observed an association between circulating anti-glycoprotein E1E2 antibodies and B cell HCV transmission. Taken together, our studies provide evidence for HCV transmission by B cells, findings that have clinical implications for prophylactic and therapeutic antibody-based vaccine design.