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A systems biology approach for diagnostic and vaccine antigen discovery in tropical infectious diseases

Liang, Li; Felgner, Philip L.

Current Opinion in Infectious Diseases: October 2015 - Volume 28 - Issue 5 - p 438–445
doi: 10.1097/QCO.0000000000000193
TROPICAL AND TRAVEL-ASSOCIATED DISEASES: Edited by Joseph M. Vinetz and Yukari C. Manabe
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Purpose of review There is a need for improved diagnosis and for more rapidly assessing the presence, prevalence, and spread of newly emerging or reemerging infectious diseases. An approach to the pathogen-detection strategy is based on analyzing host immune response to the infection. This review focuses on a protein microarray approach for this purpose.

Recent findings Here we take a protein microarray approach to profile the humoral immune response to numerous infectious agents, and to identify the complete antibody repertoire associated with each disease. The results of these studies lead to the identification of diagnostic markers and potential subunit vaccine candidates. These results from over 30 different organisms can also provide information about common trends in the humoral immune response.

Summary This review describes the implications of the findings for clinical practice or research. A systems biology approach to identify the antibody repertoire associated with infectious diseases challenge using protein microarray has become a powerful method in identifying diagnostic markers and potential subunit vaccine candidates, and moreover, in providing information on proteomic feature (functional and physically properties) of seroreactive and serodiagnostic antigens. Combining the detection of the pathogen with a comprehensive assessment of the host immune response will provide a new understanding of the correlations between specific causative agents, the host response, and the clinical manifestations of the disease.

Division of Infectious Diseases, Department of Medicine, University of California, Irvine, California, USA

Correspondence to Philip L. Felgner, Division of Infectious Diseases, Department of Medicine, University of California, Irvine, CA 92697, USA. Tel: +1 949 824 1407; fax: +1 949 824 9675; e-mail: pfelgner@uci.edu

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INTRODUCTION

A major component of the adaptive immune response to infection is the generation of protective and long-lasting humoral immunity. Analyses of antibody responses against different infectious agents are critical for diagnosing infectious diseases, understanding pathogenic mechanisms, and the development and evaluation of vaccines. Protein microarrays are well suited to identify, quantify, and compare individual antigenic responses following exposure to infectious agents. It can now evaluate antibody responses to hundreds, or even thousands, of recombinant antigens at one time. These large-scale studies have uncovered new antigenic targets, provided new insights into vaccine research and yielded an overview of immunoreactivity against almost the entire proteome of certain pathogens. This technology can be applied to the development of improved serodiagnostic tests, discovery of subunit vaccine antigen candidates, epidemiologic research, and vaccine development, as well as providing novel insights into infectious disease and the immune system. In this review, we will discuss the use of protein microarrays as a powerful tool to define the humoral immune response to bacteria and viruses.

Factors governing selection of the particular antigens recognized are unclear [1,2]. It is not uncommon for viruses encoding a small number of proteins to generate antibodies against each encoded protein. But for infectious agents containing hundreds or thousands of proteins only a subset of the proteome is recognized and little is known about the extent or the characteristics of this subset of antigens. Methods for making a complete empirical accounting of the immunoproteome have limitations, particularly when the genome of the organism is large. The Protein Microarray Laboratory at University of California Irvine has developed a highly efficient method to determine the humoral immune response to microbial antigens. We have applied this approach to more than 30 medically important infectious microorganisms [3–33] including Mycobacterium tuberculosis, Plasmodium falciparum, Plasmodium vivax, Brucella melitensis, Chlamydia trachomatis, Francisella tularensis, Burkholderia pseudomallei, Coxiella burnetii, Borrelia burgdorferi, Salmonella enterica Typhi, Rickettsia prowazekii, Rickettsia rickettsii, Orientia tsutsugamushi, Bartonella henselae, Leptospira interrogans, Toxoplasma gondii, Candida albicans, Schistosoma mansoni, and viruses including vaccinia herpes simplex viruses 1&2, varicella zoster virus, Epstein–Barr virus, human papillomaviruses, HIV, dengue, influenza, West Nile virus, yellow fever, Saint Louis encephalitis, Japanese encephalitis, and chikungunya viruses. After launching this project 10 years ago, we have made more than 40 000 plasmids, printed the encoded proteins on 25 000 microarrays and probed the arrays with 15 000 serum specimens in order to determine disease-associated antibody profiles in people infected with each agent. These chips can be probed with sera from infected patients to determine the immunodominant antigens for each agent and the methodology is amenable to the screening of sera from very large cohorts numbering in the thousands. When seroreactive and serodiagnostic antigen subsets from different infectious agents are printed onto the same array, the chip can discriminate between patients infected with different agents and also identify individuals with coinfections or multiple infections. We have shown that the individual proteins printed on these arrays capture antibodies present in serum from infected individuals and the amount of captured antibody can be quantified using fluorescent secondary antibody. In this way, a comprehensive profile of antibodies that result after infection or exposure can be determined that is characteristic of the type of infection and the stage of disease [9,10,31].

Here we summarize the approximate seroreactive and serodiagnostic antigens that were identified and published in 30 different organisms, and discuss the antibody response predictions from classification of reactive antigens based on functional and physical properties.

Box 1

Box 1

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PROTEIN MICROARRAY PRODUCTION, PROBING, AND ANALYSIS

Genes were amplified and cloned using a high-throughput PCR and recombination method [29]. Open reading frames from genomic DNA or cDNA were identified and amplified using gene-specific primers containing about 20 bp nucleotide extension complementary to ends of linearized pXT7 vector, which allows homologous recombination between the PCR product and pXT7 vector in competent Escherichia coli cells. The resulting fusion proteins also harbored a hemagglutinin epitope at the 3′ end and polyhistidine at the 5′ end. Plasmids were expressed at 24 °C in a 16 h in-vitro transcription/translation E. coli system (expressway kits from Invitrogen). For no DNA controls, no plasmid DNA was added to the same amount of reagent from in-vitro transcription/translation E. coli system to test E. coli background reactivity. For microarrays, 10 μl of reaction was mixed with 3.3 μl 0.2% Tween 20 to give a final concentration of 0.05% Tween 20, and printed onto nitrocellulose coated glass FAST slides (Whatman) using an Omni Grid 100 microarray printer (Genomic Solutions). Sera samples were diluted in E. coli lysate (Mclab). Slides were incubated in biotin-conjugated secondary antibody (Jackson ImmunoResearch) and detected by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences). Microarray slides were scanned and analyzed using a Perkin Elmer ScanArray Express HT or Genepix microarray scanner. Intensities were quantified. All signal intensities were corrected for spot-specific background. All foreground values were transformed and normalized using a robust linear model or nonlinear variance stabilizing normalization to remove systematic effects [24,34,35] (Fig. 1).

FIGURE 1

FIGURE 1

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PERCENTAGE OF SEROREACTIVE ANTIGENS

Discovery of novel antigens associated with infectious diseases is fundamental to the development of serodiagnostic tests and protein subunit vaccines against existing and emerging pathogens. Through over 10 years of effort, we have identified over 1000 antigens associated with infections or vaccinations in 30 different organisms (Table 1) [3–6,9–17,23,25▪▪,31–33,36▪,37–39,40▪▪,41,42,43▪,44,45▪,46▪,47▪▪], accounting for around 2–5% of bacterial genome; 20–57% of viral genome; and 10–45% of parasite genomes. Antigens differentially reactive among infected and healthy controls comprise even smaller percentage of the genome size: from 0.3 to 3% for bacteria; 16 to 40% for viruses, and 2 to 18% for parasites. Borrelia burgdorferi, however, generate higher antibody responses against approximately 15% of polypeptides during natural infection, of which half are differentially reactive between naturally infected and uninfected individuals [10].

Table 1

Table 1

Antigens were classified as ‘seroreactive’ with mean reactivity greater than 2–3 standard deviations above the mean of the negative controls in most organisms; and differentially reactive antigens are classified by Benjamini-Hochberg adjusted P value smaller than 0.05 by comparing the negative group with infected or vaccinated individuals.

Full proteome microarrays were constructed for only a limited number of bacterial species; however, other data were published using partial arrays containing only partial proteome, and may over-represent the percentages of seroreactive and serodiagnostic antigens in the full proteome because the subset of proteins on the array was selected based on antigenic features seen previously.

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ENRICHMENT ANALYSIS REVEALS PHYSICAL PROPERTIES AND CELLULAR FUNCTIONS ASSOCIATED WITH IMMUNOGENICITY

Another application for these empirical data is to train an algorithm to predict reactive antigens in silico, and several studies from our group apply enrichment analyses to identify proteomic features that tend to be seen more frequently in the seroreactive and serodiagnostic antigen sets [12,17,23].

Efforts to predict antigenicity have relied on a few computational algorithms predicting signal peptide sequences (signalP), transmembrane domains (TMHMM), or subcellular localization (Psort). The current database from this protein microarray approach contains quantitative antibody reactivity data against 40 000 proteins derived from 30 infectious microorganisms and more than 30 million data points derived from 15 000 patient sera. Interrogation of these data sets has revealed more than 10 proteomic features that are associated with antigenicity allowing an in-silico protein sequence and functional annotation-based approach to triage the least likely antigenic proteins from those that are more likely to be antigenic.

These proteomic enrichment features (Table 2) are: functionally annotated Clusters of Orthologous Groups of proteins (U, M, N, and O) or gene ontology function and process; computationally predicted features (TMHMM, Signal peptide, pSort Outermembrane, pSort Periplasmic, and isoelectric point (pI) less than 5 for bacteria, and pI 7–9 for parasites); and abundance of expression. This approach applied to B. melitensis predicts 37% of the bacterial proteome containing 91% of the antigens empirically identified by probing proteome microarrays [12].

Table 2

Table 2

Parasite toxoplasma gondii proteins were assigned by gene ontology functions. Proteins involved in protein binding, catalytic activity, transporter activity, and transferase activity were significantly enriched [13]. Proteins with enzymatic activity other than kinase activity were enriched at 2.0 fold, and proteins with enzyme regulator activity, structural molecule activity, and ion channel activity were also highly enriched. Proteins with gene ontology null functions, or involved in nucleotide and nucleic acid binding were underrepresented [13].

Proteins were also assigned by gene ontology process classification. Proteins involved in ATP biosynthetic process were enriched. Several proteins involved in transport were also significantly enriched, including ion transport, protein transport, vesicle mediated transport, and other transport functions. Proteins involved in metabolic process, proteolysis, and signal peptide processing were also enriched. Conversely, proteins not assigned with gene ontology process categories were significantly underrepresented (0.5 fold; P value 3.301 × 10−21) [13].

An examination with the Pf proteins on the microarray based on gene ontological analysis revealed that approximately 40% of the immunogenic proteins are expressed in the membrane of the parasite or host erythrocyte and that they are overrepresented in the biological process categories of ‘pathogenesis,’ ‘cytoadherence to microvasculature,’ ‘antigenic variation,’ and ‘rosetting’ [5].

The data set of Vaccinia viral proteins also allowed us to identify properties of viral proteins that were associated with immunogenicity. We found that membrane and core proteins, proteins with late or early/late temporal expression, and proteins with transmembrane domains were overrepresented in the immunoreactive antigen set relative to the whole proteome. These predictors are strongest in MVA profiles, as the antibody profile to MVA is more heavily skewed toward structural proteins. In contrast, early proteins were underrepresented relative to the whole proteome, and there was negligible influence of molecular weight, pI, or the presence of a signal sequence on immunogenicity. Vaccinia antigens are either abundant components of MV particles, such as A10 and L4 [48], or are expressed at high levels in infected cells, such as I1 and WR148 [49,50]. Their abundance may contribute to immunogenicity once released from infected cells, particularly if, like D13 [51], such proteins have a propensity for self-assembly into macromolecular structures.

Analysis was also done for the herpes simplex virus-1 antibody profile based on gene ontology component classifiers according to the database at www.uniprot.org. The percentage of the total number of genes assigned to each gene ontology component present in the proteome and in the seroreactive antigens was determined, and the ratio was used to determine the fold enrichment. The analysis revealed 12 proteins on the array that were assigned the gene ontology component virion membrane, of which nine were seroreactive. Tegument proteins were not enriched in the seroreactive antigen set [37].

Overall, our data show that the antibody profile is not a random assortment of specificities, but strongly biased toward the recognition of certain proteomic features. Why we do not observe antibodies to all intracellular proteins expressed from infected cells remains unclear. It is also interesting, to note, that the rules that determine immunogenicity might be different from those that define protection.

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NAIVE BAYES CLASSIFICATION

Individual proteomic features provide some information about the likelihood of a protein being seroreactive; however, using all of these features together leads to a better segregation of the hits from the rest of the proteome. To analyze the relationship between all of these features and the seroreactivity of the proteins in a rigorous manner, we used a naive Bayes formulation [52].

We applied a naive Bayes classification approach to assign a relative numerical score to each antigen in the B. melitensis (Bm) proteome. This score reflects the relative likelihood that a protein will be reactive based on its functionally annotated or computationally predicted features. Our analyses indicates that 91% of serodiagnostic antigens are predictable from the top 20% of the genome ranked by this naive Bayes classification approach, and the antigens with enriched features in the top 20% of the genome account for 100% of serodiagnostic antigens with these features. Without this naive Bayes classification approach, we would have to clone 37% of the genome with enriching features to obtain 91% of serodiagnostic antigens. This analysis greatly enhances the predictive efficiency compared with previous studies, will provide a basis for targeted screens of entire proteomes based on likelihood of seroreactivity, and help determine trends in the humoral immune response to gram-negative bacteria. The same approach has been applied to S. enterica and revealed that we would need to screen only 25% of the genome to be able to identify 72% of serodiagnostic antigens (Table 3).

Table 3

Table 3

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CONCLUSION

The development of protein arrays for profiling the antibody response generated upon exposure to an infectious agent has allowed for new insight into the humoral immune response and the identification of potential subunit vaccine candidates and new diagnostics. No other existing approach can provide such a thorough perspective of the humoral immune response to infection. Moreover, it provides a systematic foundation formation on proteomic features (functional and physically properties) of seroreactive and serodiagnostic antigens. The information presented here will allow future protein microarray screening to focus efforts on portions of the proteome that most likely contain seroreactive proteins, and may also be useful for understanding the antibody responses to bacteria, viruses, and parasites.

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Acknowledgements

None.

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Financial support and sponsorship

This work was supported by NIH grants U01AI078213, AI089686 and AI095916.

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Conflicts of interest

There are no conflicts of interest.

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REFERENCES AND RECOMMENDED READING

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • ▪ of special interest
  • ▪▪ of outstanding interest
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Keywords:

antigen; immune response; protein microarray; serodiagnostic

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