Vaccinomics and adversomics: key elements for a personalized vaccinology

Vaccines are one of the most important and effective tools in the prevention of infectious diseases and research about all the aspects of vaccinology are essential to increase the number of available vaccines more and more safe and effective. Despite the unquestionable value of vaccinations, vaccine hesitancy has spread worldwide compromising the success of vaccinations. Currently, the main purpose of vaccination campaigns is the immunization of whole populations with the same vaccine formulations and schedules for all individuals. A personalized vaccinology approach could improve modern vaccinology counteracting vaccine hesitancy and giving great benefits for human health. This ambitious purpose would be possible by facing and deepening the areas of vaccinomics and adversomics, two innovative areas of study investigating the role of a series of variables able to influence the immune response to vaccinations and the development of serious side effects, respectively. We reviewed the recent scientific knowledge about these innovative sciences focusing on genetic and non-genetic basis involved in the individual response to vaccines in terms of both immune response and side effects.

Designing, cloning and simulation studies of cancer/testis antigens based multi-epitope vaccine candidates against cutaneous melanoma: An immunoinformatics approach

Background

Melanoma is the most fatal kind of skin cancer. Among its various types, cutaneous melanoma is the most prevalent one. Melanoma cells are thought to be highly immunogenic due to the presence of distinct tumor-associated antigens (TAAs), which includes carcinoembryonic antigen (CEA), cancer/testis antigens (CTAs) and neo-antigens. The CTA family is a group of antigens that are only expressed in malignancies and testicular germ cells.

Methods

We used integrative framework and systems-level analysis to predict potential vaccine candidates for cutaneous melanoma involving epitopes prediction, molecular modeling and molecular docking to cross-validate the binding affinity and interaction between potential vaccine agents and major histocompatibility molecules (MHCs) followed by molecular dynamics simulation, immune simulation and in silico cloning.

Results

In this study, three cancer/testis antigens were targeted for immunotherapy of cutaneous melanoma. Among many CTAs that were studied for their expression in primary and malignant melanoma, NY-ESO-1, MAGE1 and SSX2 antigens are most prevalent in cutaneous melanoma. Cytotoxic and Helper epitopes were predicted, and the finest epitopes were shortlisted based on binding score. The vaccine construct was composed of the four epitope-rich domains of antigenic proteins, an appropriate adjuvant, His tag and linkers. This potential multi-epitope vaccine was further evaluated in terms of antigenicity, allergencity, toxicity and other physicochemical properties. Molecular interaction estimated through protein-protein docking unveiled good interactions characterized by favorable binding energies. Molecular dynamics simulation ensured the stability of docked complex and the predicted immune response through immune simulation revealed elevated levels of antibodies titer, cytokines, interleukins and immune cells (NK, DC and MA) population.

Conclusion

The findings indicate that the potential vaccine candidates could be effective immunotherapeutic agents that modify the treatment strategies of cutaneous melanoma.

Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine

A vaccine is defined as a biologic preparation that trains the immune system, boosts immunity, and protects against a deadly microbial infection. They have been used for centuries to combat a variety of contagious illnesses by means of subsiding the disease burden as well as eradicating the disease. Since infectious disease pandemics are a recurring global threat, vaccination has emerged as one of the most promising tools to save millions of lives and reduce infection rates. The World Health Organization reports that immunization protects three million individuals annually. Currently, multi-epitope-based peptide vaccines are a unique concept in vaccine formulation. Epitope-based peptide vaccines utilize small fragments of proteins or peptides (parts of the pathogen), called epitopes, that trigger an adequate immune response against a particular pathogen. However, conventional vaccine designing and development techniques are too cumbersome, expensive, and time-consuming. With the recent advancement in bioinformatics, immunoinformatics, and vaccinomics discipline, vaccine science has entered a new era accompanying a modern, impressive, and more realistic paradigm in designing and developing next-generation strong immunogens. In silico designing and developing a safe and novel vaccine construct involves knowledge of reverse vaccinology, various vaccine databases, and high throughput techniques. The computational tools and techniques directly associated with vaccine research are extremely effective, economical, precise, robust, and safe for human use. Many vaccine candidates have entered clinical trials instantly and are available prior to schedule. In light of this, the present article provides researchers with up-to-date information on various approaches, protocols, and databases regarding the computational designing and development of potent multi-epitope-based peptide vaccines that can assist researchers in tailoring vaccines more rapidly and cost-effectively.

Vaccinomics: A scoping review

BACKGROUND

This scoping review summarizes a key aspect of vaccinomics by collating known associations between heterogeneity in human genetics and vaccine immunogenicity and safety.

METHODS

We searched PubMed for articles in English using terms covering vaccines routinely recommended to the general US population, their effects, and genetics/genomics. Included studies were controlled and demonstrated statistically significant associations with vaccine immunogenicity or safety. Studies of Pandemrix®, an influenza vaccine previously used in Europe, were also included, due to its widely publicized genetically mediated association with narcolepsy.

FINDINGS

Of the 2,300 articles manually screened, 214 were included for data extraction. Six included articles examined genetic influences on vaccine safety; the rest examined vaccine immunogenicity. Hepatitis B vaccine immunogenicity was reported in 92 articles and associated with 277 genetic determinants across 117 genes. Thirty-three articles identified 291 genetic determinants across 118 genes associated with measles vaccine immunogenicity, 22 articles identified 311 genetic determinants across 110 genes associated with rubella vaccine immunogenicity, and 25 articles identified 48 genetic determinants across 34 genes associated with influenza vaccine immunogenicity. Other vaccines had fewer than 10 studies each identifying genetic determinants of their immunogenicity. Genetic associations were reported with 4 adverse events following influenza vaccination (narcolepsy, GBS, GCA/PMR, high temperature) and 2 adverse events following measles vaccination (fever, febrile seizure).

CONCLUSION

This scoping review identified numerous genetic associations with vaccine immunogenicity and several genetic associations with vaccine safety. Most associations were only reported in one study. This illustrates both the potential of and need for investment in vaccinomics. Current research in this field is focused on systems and genetic-based studies designed to identify risk signatures for serious vaccine reactions or diminished vaccine immunogenicity. Such research could bolster our ability to develop safer and more effective vaccines.

A Quantum Vaccinomics Approach Based on Protein-Protein Interactions

Vaccines are the most effective preventive intervention to reduce the impact of infectious diseases worldwide. In particular, tick-borne diseases represent a growing burden for human and animal health worldwide and vaccines are the most effective and environmentally sound approach for the control of vector infestations and pathogen transmission. However, the development of effective vaccines for the control of tick-borne diseases with combined vector-derived and pathogen-derived antigens is one of the limitations for the development of effective vaccine formulations. Quantum biology arise from findings suggesting that living cells operate under non-trivial features of quantum mechanics, which has been proposed to be involved in DNA mutation biological process. Then, the electronic structure of the molecular interactions behind peptide immunogenicity led to quantum immunology and based on the definition of the photon as a quantum of light, the immune protective epitopes were proposed as the immunological quantum. Recently, a quantum vaccinomics approach was proposed based on the characterization of the immunological quantum to further advance the design of more effective and safe vaccines. In this chapter, we describe methods of the quantum vaccinomics approach based on proteins with key functions in cell interactome and regulome of vector-host-pathogen interactions for the identification by yeast two-hybrid screen and the characterization by in vitro protein-protein interactions and musical scores of protein interacting domains, and the characterization of conserved protective epitopes in protein interacting domains. These results can then be used for the design and production of chimeric protective antigens.

Vaccination in the context of the COVID-19 pandemic

In this review, we described the history of vaccination, the different types of vaccines, and how vaccination coverage has been affected by the current COVID-19 pandemic. The effectiveness of the vaccines under metabolic host conditions is analyzed, especially when people have lost their immunocompetence, such as in patients with chronic kidney disease who are in dialysis treatment. Vaccines are produced in a variety of industrial methods, modifying costs. The novel field of vaccinomics includes the set of immune responses, the satisfactory levels of neutralizing antibodies, the production of metabolites, and the induction of protein expression. Finally, an analysis is made of the confusing messages regarding vaccination that are disseminated on social networks, and general recommendations are given.

Vaccinomics: a cross-sectional survey of public values

Objective: We characterize public values regarding vaccinomics, which aims to improve vaccine safety and effectiveness using genomics.Methods: Panel survey (2020) of ≥18-year-olds with embedded animation introduced vaccinomics. Sociodemographic, health, and vaccination-related items were adapted from validated scales. Novel items measured trust in public health authorities, vaccinomics-related values, and preferences for federal funding: vaccinomics compared with vaccine issues and chronic diseases. Beginning and end of survey confidence in vaccine safety was measured to assess potential changes. Data were weighted to the U.S. Census. Vaccinomics-related concerns were stratified by sociodemographic characteristics, vaccine hesitancy status (composite outcome), reported serious vaccine reactions, and trust in public health authorities (PHA). Log binomial regression models estimated associations between these variables and agency to make vaccine-related decisions.Results: Most (70.7%, N = 1,925) respondents expected vaccinomics would increase their vaccine confidence compared to now. Agreement was highest among those without serious vaccine reaction experience (unexperienced: 74.2% versus experienced: 62.3%), with high trust in PHA (high: 83.3% versus low: 57.4%), and low vaccine hesitancy among parents of teenagers (low: 78.8% versus high: 62.5%) and adults without minor children (low: 79.8% versus high: 60.6%; all p < .01). Belief that vaccination was an individual's choice was associated with reported serious reactions (adjusted Prevalence Ratio (aPR): 1.16; 95% CI: 1.07, 1.25) and low trust (aPR: 0.91; 0.84, 0.98). Beginning versus end of survey vaccine safety perceptions were similar.Conclusion: Federal funding, communications, and policies should assure the public that vaccinomics will not remove their decision-making power and engender trust in PHA.

HantavirusesDB: Vaccinomics and RNA-based therapeutics database for the potentially emerging human respiratory pandemic agents

Hantaviruses are etiological agents of several severe respiratory illnesses in humans and their human-to-human transmission has been reported. To cope with any potential pandemic, this group of viruses needs further research and a data platform. Therefore, herein we developed a database "HantavirusesDB (HVdb)", where genomics, proteomics, immune resource, RNAi based therapeutics and information on the 3D structures of druggable targets of the Orthohantaviruses are provided on a single platform. The database allows the researchers to effectively map the therapeutic strategies by designing multi-epitopes subunit vaccine and RNA based therapeutics. Moreover, the ease of the web interface allow the users to retrieve specific information from the database. Because of the high quality and excellent functionality of the HVdb, therapeutic research of Hantaviruses can be accelerated, and data analysis might be a foundation to design better treatment strategies targeting the hantaviruses. The database is accessible at http://hvdb.dqweilab-sjtu.com/index.php.

RNA-seq analysis and gene expression dynamics in the salivary glands of the argasid tick Ornithodoros erraticus along the trophogonic cycle

BACKGROUND

The argasid tick Ornithodoros erraticus is the main vector of tick-borne human relapsing fever (TBRF) and African swine fever (ASF) in the Mediterranean Basin. Tick salivary proteins secreted to the host at the feeding interface play critical roles for tick feeding and may contribute to host infection by tick-borne pathogens; accordingly, these proteins represent interesting antigen targets for the development of vaccines aimed at the control and prevention of tick infestations and tick-borne diseases.

METHODS

To identify these proteins, the transcriptome of the salivary glands of O. erraticus was de novo assembled and the salivary gene expression dynamics assessed throughout the trophogonic cycle using Illumina sequencing. The genes differentially upregulated after feeding were selected and discussed as potential antigen candidates for tick vaccines.

RESULTS

Transcriptome assembly resulted in 22,007 transcripts and 18,961 annotated transcripts, which represent 86.15% of annotation success. Most salivary gene expression took place during the first 7 days after feeding (2088 upregulated transcripts), while only a few genes (122 upregulated transcripts) were differentially expressed from day 7 post-feeding onwards. The protein families more abundantly overrepresented after feeding were lipocalins, acid and basic tail proteins, proteases (particularly metalloproteases), protease inhibitors, secreted phospholipases A2, 5'-nucleotidases/apyrases and heme-binding vitellogenin-like proteins. All of them are functionally related to blood ingestion and regulation of host defensive responses, so they can be interesting candidate protective antigens for vaccines.

CONCLUSIONS

The O. erraticus sialotranscriptome contains thousands of protein coding sequences-many of them belonging to large conserved multigene protein families-and shows a complexity and functional redundancy similar to those observed in the sialomes of other argasid and ixodid tick species. This high functional redundancy emphasises the need for developing multiantigenic tick vaccines to reach full protection. This research provides a set of promising candidate antigens for the development of vaccines for the control of O. erraticus infestations and prevention of tick-borne diseases of public and veterinary health relevance, such as TBRF and ASF. Additionally, this transcriptome constitutes a valuable reference database for proteomics studies of the saliva and salivary glands of O. erraticus.

Vaccinomics approach for scheming potential epitope-based peptide vaccine by targeting l-protein of Marburg virus

Marburg virus is one of the world’s most threatening diseases, causing extreme hemorrhagic fever, with a death rate of up to 90%. The Food and Drug Administration (FDA) currently not authorized any treatments or vaccinations for the hindrance and post-exposure of the Marburg virus. In the present study, the vaccinomics methodology was adopted to design a potential novel peptide vaccine against the Marburg virus, targeting RNA-directed RNA polymerase (l). A total of 48 l-proteins from diverse variants of the Marburg virus were collected from the NCBI GenBank server and used to classify the best antigenic protein leading to predict equally T and B-cell epitopes. Initially, the top 26 epitopes were evaluated for the attraction with major histocompatibility complex (MHC) class I and II alleles. Finally, four prospective central epitopes NLSDLTFLI, FRYEFTRHF, YRLRNSTAL, and YRVRNVQTL were carefully chosen. Among these, FRYEFTRHF and YRVRNVQTL peptides showed 100% conservancy. Though YRLRNSTAL showed 95.74% conservancy, it demonstrated the highest combined score as T cell epitope (2.5461) and population coverage of 94.42% among the whole world population. The epitope was found non-allergenic, and docking interactions with human leukocyte antigens (HLAs) also verified. Finally, in vivo analysis of the recommended peptides might contribute to the advancement of an efficient and exclusively prevalent vaccine that would be an active route to impede the virus spreading.

Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics

The emergence and rapid expansion of the coronavirus disease (COVID-19) require the development of effective countermeasures especially a vaccine to provide active acquired immunity against the virus. This study presented a comprehensive vaccinomics approach applied to the complete protein data published so far in the National Center for Biotechnological Information (NCBI) coronavirus data hub. We identified non-structural protein 8 (Nsp8), 3C-like proteinase, and spike glycoprotein as potential targets for immune responses to COVID-19. Epitopes prediction illustrated both B-cell and T-cell epitopes associated with the mentioned proteins. The shared B and T-cell epitopes: DRDAAMQRK and QARSEDKRA of Nsp8, EDMLNPNYEDL and EFTPFDVVR of 3C-like proteinase, and VNNSYECDIPI of the spike glycoprotein are regions of high potential interest and have a high likelihood of being recognized by the human immune system. The vaccine construct of the epitopes shows stimulation of robust primary immune responses and high level of interferon gamma. Also, the construct has the best conformation with respect to the tested innate immune receptors involving vigorous molecular mechanics and solvation energy. Designing of vaccination strategies that target immune response focusing on these conserved epitopes could generate immunity that not only provide cross protection across Betacoronaviruses but additionally resistant to virus evolution.

Reverse Vaccinology and Its Applications

The application of the fields of pharmacogenomics and pharmacogenetics to vaccine design, profoundly combined with bioinformatics, has been recently termed "vaccinomics." The enormous amount of information generated by whole genome sequencing projects and the rise of bioinformatics has triggered the birth of a new era of vaccine research and development, leading to a "third generation" of vaccines, which are based on the application of vaccinomics science to vaccinology. The first example of such an approach is reverse vaccinology. Reverse vaccinology reduces the period of vaccine target detection and evaluation to 1-2 years. This approach targets the genomic sequence and predicts those antigens that are most likely to be vaccine candidates. This approach allows not only the identification of all the antigens obtained by the previous methods but also the discovery of new antigens that work on a totally different paradigm. Hence this method helps in the discovery of novel mechanisms of immune intervention. Epitope-based immune-derived vaccines (IDV) are generally considered to be safe when compared to other vectored or attenuated live vaccines. Epitope-based IDV may also provide essential T-cell help for antibody-directed vaccines. Such vaccines may have a significant advantage over earlier vaccine design approaches, as the cautious assortment of the components may diminish.

Vaccines, adjuvants and autoimmunity

Vaccines and autoimmunity are linked fields. Vaccine efficacy is based on whether host immune response against an antigen can elicit a memory T-cell response over time. Although the described side effects thus far have been mostly transient and acute, vaccines are able to elicit the immune system towards an autoimmune reaction. The diagnosis of a definite autoimmune disease and the occurrence of fatal outcome post-vaccination have been less frequently reported. Since vaccines are given to previously healthy hosts, who may have never developed the disease had they not been immunized, adverse events should be carefully accessed and evaluated even if they represent a limited number of occurrences. In this review of the literature, there is evidence of vaccine-induced autoimmunity and adjuvant-induced autoimmunity in both experimental models as well as human patients. Adjuvants and infectious agents may exert their immune-enhancing effects through various functional activities, encompassed by the adjuvant effect. These mechanisms are shared by different conditions triggered by adjuvants leading to the autoimmune/inflammatory syndrome induced by adjuvants (ASIA syndrome). In conclusion, there are several case reports of autoimmune diseases following vaccines, however, due to the limited number of cases, the different classifications of symptoms and the long latency period of the diseases, every attempt for an epidemiological study has so far failed to deliver a connection. Despite this, efforts to unveil the connection between the triggering of the immune system by adjuvants and the development of autoimmune conditions should be undertaken. Vaccinomics is a field that may bring to light novel customized, personalized treatment approaches in the future.

Vaccinomics, adversomics, and the immune response network theory: individualized vaccinology in the 21st century

Vaccines, like drugs and medical procedures, are increasingly amenable to individualization or personalization, often based on novel data resulting from high throughput "omics" technologies. As a result of these technologies, 21st century vaccinology will increasingly see the abandonment of a "one size fits all" approach to vaccine dosing and delivery, as well as the abandonment of the empiric "isolate-inactivate-inject" paradigm for vaccine development. In this review, we discuss the immune response network theory and its application to the new field of vaccinomics and adversomics, and illustrate how vaccinomics can lead to new vaccine candidates, new understandings of how vaccines stimulate immune responses, new biomarkers for vaccine response, and facilitate the understanding of what genetic and other factors might be responsible for rare side effects due to vaccines. Perhaps most exciting will be the ability, at a systems biology level, to integrate increasingly complex high throughput data into descriptive and predictive equations for immune responses to vaccines. Herein, we discuss the above with a view toward the future of vaccinology.

HIV-2 and its role in conglutinated approach towards Acquired Immunodeficiency Syndrome (AIDS) Vaccine Development

Acquired Immunodeficiency Syndrome (AIDS) is one of the most critically acclaimed endemic diseases, caused by two lentiviruses HIV-1 and 2. HIV-2 displays intimate serological and antigenic resemblance to Simian Immunodeficiency Virus (SIV) along with less pathogenicity, lower infectivity and appreciable cross reactivity with HIV-1 antigens. The present era is confronted with the challenge to fabricate a vaccine effective against all clades of both the species of HIV. But vaccine development against HIV-1 has proven highly intricate, moreover the laborious and deficient conventional approaches has slackened the pace regarding the development of new vaccines. These concerns may be tackled with the development of HIV-2 vaccine as a natural control of HIV-1 that has been found in ancestors of HIV-2 i.e. African monkeys, mangabeys and macaques. Thereby, suggesting the notion of cross protection among HIV-2 and HIV-1. Assistance of bioinformatics along with vaccinomics strategy can bring about a quantum leap in this direction for surpassing the bottleneck in conventional approaches. These specifics together can add to our conception that HIV-2 vaccine design by in silico strategy will surely be a constructive approach for HIV-1 targeting.