Biotechnology and vaccines: application of functional genomics to Neisseria meningitidis and other bacterial pathogens

Since its introduction, vaccinology has been very effective in preventing infectious diseases. However, in several cases, the conventional approach to identify protective antigens, based on biochemical, immunological and microbiological methods, has failed to deliver successful vaccine candidates against major bacterial pathogens. The recent development of powerful biotechnological tools applied to genome-based approaches has revolutionized vaccine development, biological research and clinical diagnostics. The availability of a genome provides an inclusive virtual catalogue of all the potential antigens from which it is possible to select the molecules that are likely to be more effective. Here, we describe the use of "reverse vaccinology", which has been successful in the identification of potential vaccines candidates against Neisseria meningitidis serogroup B and review the use of functional genomics approaches as DNA microarrays, proteomics and comparative genome analysis for the identification of virulence factors and novel vaccine candidates. In addition, we describe the potential of these powerful technologies in understanding the pathogenesis of various bacteria.     

Pathogen proteins eliciting antibodies do not share epitopes with host proteins: a bioinformatics approach

The best way to prevent diseases caused by pathogens is by the use of vaccines. The advent of genomics enables genome-wide searches of new vaccine candidates, called reverse vaccinology. The most common strategy to apply reverse vaccinology is by designing subunit recombinant vaccines, which usually generate an humoral immune response due to B-cell epitopes in proteins. A major problem for this strategy is the identification of protective immunogenic proteins from the surfome of the pathogen. Epitope mimicry may lead to auto-immune phenomena related to several human diseases. A sequence-based computational analysis has been carried out applying the BLASTP algorithm. Therefore, two huge databases have been created, one with the most complete and current linear B-cell epitopes, and the other one with the surface-protein sequences of the main human respiratory bacterial pathogens. We found that none of the 7353 linear B-cell epitopes analysed shares any sequence identity region with human proteins capable of generating antibodies, and that only 1% of the 2175 exposed proteins analysed contain a stretch of shared sequence with the human proteome. These findings suggest the existence of a mechanism to avoid autoimmunity. We also propose a strategy for corroborating or warning about the viability of a protein linear B-cell epitope as a putative vaccine candidate in a reverse vaccinology study; so, epitopes without any sequence identity with human proteins should be very good vaccine candidates, and the other way around.     

The role of structural proteomics in vaccine development: recent advances and future prospects

Vaccines are the most effective way to fight infectious diseases saving countless lives since their introduction. Their evolution during the last century made use of the best technologies available to continuously increase their efficacy and safety. Mass spectrometry (MS) and proteomics are already playing a central role in the identification and characterization of novel antigens. Over the last years, we have been witnessing the emergence of structural proteomics in vaccinology, as a major tool for vaccine candidate discovery, antigen design and life cycle management of existing products. In this review, we describe the MS techniques associated to structural proteomics and we illustrate the contribution of structural proteomics to vaccinology discussing potential applications.     

Reverse vaccinology

Biochemical, serological and microbiological methods have been used to dissect pathogens and identify the components useful for vaccine development. Although successful in many cases, this approach is time-consuming and fails when the pathogens cannot be cultivated in vitro, or when the most abundant antigens are variable in sequence. Now genomic approaches allow prediction of all antigens, independent of their abundance and immunogenicity during infection, without the need to grow the pathogen in vitro. This allows vaccine development using non-conventional antigens and exploiting non-conventional arms of the immune system. Many vaccines impossible to develop so far will become a reality. Since the process of vaccine discovery starts in silico using the genetic information rather than the pathogen itself, this novel process can be named reverse vaccinology.     

Viral vaccines and their manufacturing cell substrates: New trends and designs in modern vaccinology

Vaccination is one of the most effective interventions in global health. The worldwide vaccination programs significantly reduced the number of deaths caused by infectious agents. A successful example was the eradication of smallpox in 1979 after two centuries of vaccination campaigns. Since the first variolation administrations until today, the knowledge on immunology has increased substantially. This knowledge combined with the introduction of cell culture and DNA recombinant technologies revolutionized vaccine design. This review will focus on vaccines against human viral pathogens, recent developments on vaccine design and cell substrates used for their manufacture. While the production of attenuated and inactivated vaccines requires the use of the respective permissible cell substrates, the production of recombinant antigens, virus‐like particles, vectored vaccines and chimeric vaccines requires the use – and often the development – of specific cell lines. Indeed, the development of novel modern viral vaccine designs combined with, the stringent safety requirements for manufacture, and the better understanding on animal cell metabolism and physiology are increasing the awareness on the importance of cell line development and engineering areas. A new era of modern vaccinology is arriving, offering an extensive toolbox to materialize novel and creative ideas in vaccine design and its manufacture.     

Role of proteins of the macroglobulin family in the mechanisms of infection

Information on the properties of proteins of the macroglobulin family taking part in the host protection from viral, fungal and bacterial pathogens is reviewed. High plasticity and polyfunctional character of these proteins makes it possible to realize different protective functions. They inhibit the lysis of the cell wall by binding the hydrolases of the pathogen thus blocking its penetration into the cell, directly participate in the presentation of antigens to immunocompetent cells, transport antibacterial substances (interferons, lysozyme) to the zone of infection. In addition, macroglobulins take part in the apoptosis regulation in infected cells, utilization of the lysosomal enzymes of annihilated pathogens. The complexes of macroglobulins with some proteins are powerful inductors of antibody production. Further studies of the properties of these proteins will result in a better understanding of the nature of infectious process. The possibility of artificial formation of macroglobulin complexes with pathogen components or with substances possessing protective or anti-inflammatory properties opens prospects for using these proteins in the fields of vaccinology, gene therapy and molecular biology.     

Proteomic study of non-typable Haemophilus influenzae

Non-typable Haemophilus influenzae (NTHi) are small, gram-negative bacteria and are strictly human pathogens, causing acute otitis media, sinusitis and community-acquired pneumonia. There is no vaccine available for NTHi, as there is for H. influenzae type b. Recent advances in proteomic techniques are finding novel applications in the field of vaccinology. There are several protein separation techniques available today, each with inherent advantages and disadvantages. We employed a combined proteomics approach, including sequential extraction and analytical two-dimensional polyacrylamide electrophoresis (2D PAGE), and two-dimensional semi-preparative electrophoresis (2D PE), in order to study protein expression in the A4 NTHi strain. Although putative vaccine candidates were identified with both techniques, 11 of 15 proteins identified using the 2D PE approach were not identified by 2D PAGE, demonstrating the complementarily of the two methods.     

Bacterial proteomics and identification of potential vaccine targets

Currently, the greatest causes of human morbidity and mortality are infectious diseases. Vaccination remains the most effective measure to lessen this burden on the human population. Many vaccines presently in use were developed using techniques first proposed by Louis Pasteur, which involved the use of inactivated, attenuated live forms, or extracts of pathogenic organisms to immunize the host and provide protection from the disease. The advent of the genomic era has recently led to a new generation of rationally designed vaccines developed using a process termed reverse vaccinology. This approach uses genomic data in silico to identify proteins encoded by the pathogen as potential vaccine candidates. Proteomic technologies serve as an important complement to the reverse vaccinology approach to antigen discovery. Proteomic techniques are able to identify proteins that are expressed by the pathogen during infection of a host and the subset of proteins that reside on the surface of the pathogen. These two traits should be considered central factors to vaccine antigen selection as they assure that the host will be able to mount an effective immune response that leads to lasting protection from the pathogen.     

Systems vaccinology: a promise for the young and the poor

As a child, the risk of suffering and dying from infection is higher the younger you are; and higher, the less developed a region you are born in. Childhood vaccination programmes have greatly reduced mortality around the world, but least so for the very young among the very poor of the world. This appears partly owing to suboptimal vaccine effectiveness. Unfortunately, although most vaccines are administered to the newborn and very young infant (less than or equal to two months), we know the least about their host response to vaccination. We thus currently lack the knowledge to guide efforts aimed at improving vaccine effectiveness in this vulnerable population. Systems vaccinology, the study of molecular networks activated by immunization, has begun to provide unprecedented insights into mechanisms leading to vaccine-induced protection from infection or disease. However, all published reports of systems vaccinology have focused on either adults or at most children and older infants, not those most in need, i.e. newborns and very young infants. Given that the tools of systems vaccinology work perfectly well with very small sample volumes, it is time we deliver the promise that systems vaccinology holds for those most in need of vaccine-mediated protection from infection.     

Genome-wide screening and identification of antigens for rickettsial vaccine development

The capacity to identify immunogens for vaccine development by genome-wide screening has been markedly enhanced by the availability of microbial genome sequences coupled to proteomic and bioinformatic analysis. Critical to this approach is in vivo testing in the context of a natural host–pathogen relationship, one that includes genetic diversity in the host as well as among pathogen strains. We aggregate the results of three independent genome-wide screens using in vivo immunization and protection against Anaplasma marginale as a model for discovery of vaccine antigens for rickettsial pathogens. In silico analysis identified 62 outer membrane proteins (Omp) from the 949 predicted proteins in the A. marginale genome. These 62 Omps were reduced to 10 vaccine candidates by two independent genome-wide screens using IgG2 from vaccinates protected from challenge following vaccination with outer membranes (screen 1) or bacterial surface complexes (screen 2). Omps with broadly conserved epitopes were identified by immunization with a live heterologous vaccine, A. marginale ssp. centrale (screen 3), reducing the candidates to three. The genome-wide screens identified Omps that have orthologs broadly conserved among rickettsial pathogens, highlighted the importance of identifying immunologically subdominant antigens, and supported the use of reverse vaccinology approaches in vaccine development for rickettsial diseases.     

流感疫苗研制的新策略

流感病毒感染可引起急性呼吸道传染病,严重危害人类的健康与生命。疫苗免疫是防控流感的重要手段。目前广泛应用的传统灭活疫苗和减毒活疫苗,在预防流感中发挥了重要作用,但存在通用性差和免疫效率低等不足。研制更为安全高效特别是能针对多种流感亚型的新型广谱疫苗成为当前流感疫苗研究的热点。随着结构生物学和反向遗传生物学等新技术的迅速发展,一些新策略不断应用于新型流感疫苗的研究,显示出良好的应用前景。     

Designing the next generation of vaccines for global public health

Vaccine research and development are experiencing a renaissance of interest from the global scientific community. There are four major reasons for this: (1) the lack of efficacious treatment for many devastating infections; (2) the emergence of multidrug resistant bacteria; (3) the need for improving the safety of the more traditional licensed vaccines; and finally, (4) the great promise for innovative vaccine design and research with convergence of omics sciences, such as genomics, proteomics, immunomics, and vaccinology. Our first project based on omics was initiated in 2000 and was termed reverse vaccinology. At that time, antigen identification was mainly based on bioinformatic analysis of a singular genome. Since then, omics-guided approaches have been applied to its full potential in several proof-of-concept studies in the industry, with the first reverse vaccinology-derived vaccine now in late stage clinical trials and several vaccines developed by omics in preclinical studies. In the meantime, vaccine discovery and development has been further improved with the support of proteomics, functional genomics, comparative genomics, structural biology, and most recently vaccinomics. We illustrate in this review how omics biotechnologies and integrative biology are expected to accelerate the identification of vaccine candidates against difficult pathogens for which traditional vaccine development has thus far been failing, and how research will provide safer vaccines and improved formulations for immunocompromised patients in the near future. Finally, we present a discussion to situate omics-guided rational vaccine design in the broader context of global public health and how it can benefit citizens in both developed and developing countries.     

New technologies for vaccine development

Despite important success of preventive vaccination in eradication of smallpox and in reduction in incidence of poliomyelitis and measles, infectious diseases remain the principal cause of mortality in the world. Technologies used in the development of vaccines used so far, mostly based on empirical approaches, are limited and insufficient to fight diseases like malaria, acquired immunodeficiency syndrome (AIDS) or adult tuberculosis. Until recently, technologies for making vaccines were based on live attenuated microorganisms, whole killed microorganisms and subunit vaccines such as purified toxoids. Fortunately, the recent advances in the understanding of host-pathogen interaction as well as our increasing knowledge of how immune responses are triggered and regulated have opened almost unlimited possibilities of developing new immunization strategies based on recombinant microorganisms or recombinant polypeptides or bacterial or viral vectors, synthetic peptides, natural or synthetic polysaccharides or plasmid DNA. Thus, considering the expending number of technologies available for making vaccines, it becomes possible for the first time in the history of vaccinology to design vaccines based on a rational approach and leading to increased efficacy and safety.     

精准设计疫苗

疫苗的出现极大降低了感染性疾病的发病率和死亡率,显著保障了全球公共健康。本文系统回顾了疫苗的发展史,分析归纳了各类型疫苗的优缺点,并介绍了本实验室构建的一类具有广谱保护性的新型疫苗--精准设计疫苗。精准设计疫苗是一类应用高通量技术和反向遗传学技术,定向筛选病原体全基因组内特异位点、区域,进而精准设计的重组疫苗。基于个体基因、环境、生活方式等特征的精准医学引领了新一轮的医疗变革,而这种基于病原体或异常细胞的特定基因、蛋白、通路的精准设计疫苗则为疫苗的研发提供了全新的技术和思路,将推动疫苗学进入新时代。     

Computer aided selection of candidate vaccine antigens

Immunoinformatics is an emergent branch of informatics science that long ago pullulated from the tree of knowledge that is bioinformatics. It is a discipline which applies informatic techniques to problems of the immune system. To a great extent, immunoinformatics is typified by epitope prediction methods. It has found disappointingly limited use in the design and discovery of new vaccines, which is an area where proper computational support is generally lacking. Most extant vaccines are not based around isolated epitopes but rather correspond to chemically-treated or attenuated whole pathogens or correspond to individual proteins extract from whole pathogens or correspond to complex carbohydrate. In this chapter we attempt to review what progress there has been in an as-yet-underexplored area of immunoinformatics: the computational discovery of whole protein antigens. The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. We begin our review by placing antigen prediction firmly into context, exploring the role of reverse vaccinology in the design and discovery of vaccines. We also highlight several competing yet ultimately complementary methodological approaches: sub-cellular location prediction, identifying antigens using sequence similarity, and the use of sophisticated statistical approaches for predicting the probability of antigen characteristics. We end by exploring how a systems immunomics approach to the prediction of immunogenicity would prove helpful in the prediction of antigens.     

Omics tools enabling vaccine discovery against fasciolosis

In the past decade significant advances in our understanding of liver fluke biology have been made through in-depth interrogation and analysis of evolving Fasciola hepatica and Fasciola gigantica omics datasets. This information is crucial for developing novel control strategies, particularly vaccines necessitated by the global spread of anthelmintic resistance. Distilling them down to a manageable number of testable vaccines requires combined rational, empirical, and collaborative approaches. Despite a lack of clear outstanding vaccine candidate(s), we must continue to identify salient parasite–host interacting molecules, likely in the secretory products, tegument, or extracellular vesicles, and perform robust trials especially in livestock, using present and emerging vaccinology technologies to discover that elusive liver fluke vaccine. Omics tools are bringing this prospect ever closer.     

DNA microarrays in the clinic: infectious diseases

We argue that the most-promising area of clinical application of microarrays in the foreseeable future is the diagnostics and monitoring of infectious diseases. Microarrays for the detection and characterization of human pathogens have already found their way into clinical practice in some countries. After discussing the persistent, yet often underestimated, importance of infectious diseases for public health, we consider the technologies that are best suited for the detection and clinical investigation of pathogens. Clinical application of microarray technologies for the detection of mycobacteria, Bacillus anthracis, HIV, hepatitis and influenza viruses, and other major pathogens, as well as the analysis of their drug-resistance patterns, illustrate our main thesis.