Time for T? Immunoinformatics addresses the challenges of vaccine design for neglected tropical and emerging infectious diseases

Vaccines have been invaluable for global health, saving lives and reducing healthcare costs, while also raising the quality of human life. However, newly emerging infectious diseases (EID) and more well-established tropical disease pathogens present complex challenges to vaccine developers; in particular, neglected tropical diseases, which are most prevalent among the world’s poorest, include many pathogens with large sizes, multistage life cycles and a variety of nonhuman vectors. EID such as MERS-CoV and H7N9 are highly pathogenic for humans. For many of these pathogens, while their genomes are available, immune correlates of protection are currently unknown. These complexities make developing vaccines for EID and neglected tropical diseases all the more difficult. In this review, we describe the implementation of an immunoinformatics-driven approach to systematically search for key determinants of immunity in newly available genome sequence data and design vaccines. This approach holds promise for the development of 21st century vaccines, improving human health everywhere

Time for T? Immunoinformatics Addresses Vaccine Design for Neglected Tropical and Emerging Infectious Diseases

Vaccines have been invaluable for global health, saving lives and reducing healthcare costs, while also raising the quality of human life. However, newly emerging infectious diseases (EID) and more well-established tropical disease pathogens present complex challenges to vaccine developers; in particular, neglected tropical diseases, which are most prevalent among the world\u27s poorest, include many pathogens with large sizes, multistage life cycles and a variety of nonhuman vectors. EID such as MERS-CoV and H7N9 are highly pathogenic for humans. For many of these pathogens, while their genomes are available, immune correlates of protection are currently unknown. These complexities make developing vaccines for EID and neglected tropical diseases all the more difficult. In this review, we describe the implementation of an immunoinformatics-driven approach to systematically search for key determinants of immunity in newly available genome sequence data and design vaccines. This approach holds promise for the development of 21st century vaccines, improving human health everywhere

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

Concept and application of a computational vaccinology workflow

BACKGROUND : The last years have seen a renaissance of the vaccine area, driven by clinical needs in infectious diseases but also chronic diseases such as cancer and autoimmune disorders. Equally important are technological improvements involving nano-scale delivery platforms as well as third generation adjuvants. In parallel immunoinformatics routines have reached essential maturity for supporting central aspects in vaccinology going beyond prediction of antigenic determinants. On this basis computational vaccinology has emerged as a discipline aimed at ab-initio rational vaccine design.Here we present a computational workflow for implementing computational vaccinology covering aspects from vaccine target identification to functional characterization and epitope selection supported by a Systems Biology assessment of central aspects in host-pathogen interaction. We exemplify the procedures for Epstein Barr Virus (EBV), a clinically relevant pathogen causing chronic infection and suspected of triggering malignancies and autoimmune disorders. RESULTS : We introduce pBone/pView as a computational workflow supporting design and execution of immunoinformatics workflow modules, additionally involving aspects of results visualization, knowledge sharing and re-use. Specific elements of the workflow involve identification of vaccine targets in the realm of a Systems Biology assessment of host-pathogen interaction for identifying functionally relevant targets, as well as various methodologies for delineating B- and T-cell epitopes with particular emphasis on broad coverage of viral isolates as well as MHC alleles.Applying the workflow on EBV specifically proposes sequences from the viral proteins LMP2, EBNA2 and BALF4 as vaccine targets holding specific B- and T-cell epitopes promising broad strain and allele coverage. CONCLUSION : Based on advancements in the experimental assessment of genomes, transcriptomes and proteomes for both, pathogen and (human) host, the fundaments for rational design of vaccines have been laid out. In parallel, immunoinformatics modules have been designed and successfully applied for supporting specific aspects in vaccine design. Joining these advancements, further complemented by novel vaccine formulation and delivery aspects, have paved the way for implementing computational vaccinology for rational vaccine design tackling presently unmet vaccine challenges

Immunopathogenesis of Orthopoxviridae: insights into immunology from smallpox to monkeypox (mpox)

Since 2019, notable global viral outbreaks have occurred necessitating further research and healthcare system investigations. Following the coronavirus disease 2019 (COVID-19) pandemic, in 2022, whilst severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains evolved, monkeypox virus (MPXV) infections became more evident. MPXV is of the Orthopoxviridae genus, belonging to the family Poxviridae. Zoonotic transmission (animal-to-human transmission) may occur. The Orthopoxviridae genus includes other orthopoxviruses (OPXVs) present in animal host reservoirs that include cowpox viruses (CPXVs), vaccinia virus (VACV), and variola virus (VARV), with the latter being a causal agent of smallpox and excessive mortality. This review aims to present facts about MPXV-specific pathogenesis, epidemiology, and immunology alongside historical perspectives. MPXV was rarely reported outside Africa before April 2000. Early research since 1796 contributed towards the eradication of VARV leading to immunisation strategies. The World Health Organisation (WHO) announcement that VARV had been eradicated was confirmed in 1980. On the 23rd of July 2022, the WHO announced MPXV as a health emergency. Therefore, concern due to the propagation of MPXV causing monkeypox (mpox) disease requires clarity. Infected hosts display symptoms like extensive cellular-initiated rashes and lesions. Infection with MPXV makes it difficult to differentiate from other diseases or skin conditions. Antiviral therapeutic drugs were typically prescribed for smallpox and mpox disease; however, the molecular and immunological mechanisms with cellular changes remain of interest. Furthermore, no official authorized treatment exists for mpox disease. Some humans across the globe may be considered at risk. Historically, presenting symptoms of mpox resemble other viral diseases. Symptoms include rashes or lesions like Streptococcus, but also human herpes viruses (HHVs), including Varicella zoster virus (VZV)

Influenza Virus-specific CD8+ T Cells

Influenza viruses are among the leading causes of acute respiratory tract infections worldwide. Natural influenza virus infections elicit both humoral and cellular immune responses. Although, neutralizing antibodies directed to the hemagglutinin (HA) globular head domain prevent reinfection with the same influenza virus they exert limited/no cross-reactivity with antigenically drifted variants or influenza viruses of different strains, it is therefore of interest to identify other correlates of protection. Cellular immunity, especially influenza virus-specific CD8+ cytotoxic T lymphocytes (CTLs), contribute to rapid clearance of influenza virus infections and thereby reduce viral shedding. Influenza virus-specific CTLs, elicited after seasonal influenza virus infections, are mainly directed to conserved internal proteins. In this dissertation we were able to demonstrate the cross-reactivity of seasonal influenza virus-specific CTLs with the novel and potentially pandemic A/H7N9 virus and between different lineages of influenza B viruses. Furthermore, using an unique PBMC donor cohort we were able to assess the longevity of these cells in healthy individuals. In addition, we were able to demonstrate that human influenza A viruses can impair the recognition of the HLA-A*0201 restricted and highly conserved M158-66 epitope by specific CTLs by variations in the extra-epitopic amino acids. This CTL evasion strategy may have implications for the viral replication kinetics in HLA-A*0201 individuals and thus the spread of influenza A viruses in the human population. Finally, we describe a novel adjuvant, G3/DT, that improves the immunogenicity of a standard inactivated seasonal influenza vaccine in terms of enhancing the antibody response and inducing a protective CTL response

Antigenic diversity of dengue virus: implications for vaccine design

Ph.DDOCTOR OF PHILOSOPH

An immunoinformatics approach for identification and characterization of T cell-mediated heterologous immunity between RNA viruses and allergens

Asthma ist eine der bedeutendsten chronischen Entzündungserkrankungen weltweit. Infektionen mit respiratorischen Viren sowie die Expositionen mit Allergenen stellen wichtige Risikofaktoren für die Entwicklung von Asthma dar. Unsere Arbeitsgruppe hat kürzlich einen Influenzavirus-vermittelten protektiven Effekt gegenüber experimentellem Asthma in einem Mausmodell gezeigt, welcher abhängig von kreuzreaktiven T-Effektor-Gedächtniszellen war. Die Hypothese dieser Forschungsarbeit war, dass die virusvermittelte heterologe Immunantwort ein breit anwendbares Konzept für verschiedene Atemwegsviren und Umweltallergene ist. Diese Immunantwort könnte durch kreuzreaktive virusspezifische T-Gedächtniszellen vermittelt werden, die bei Allergenexposition mit einer T1-gesteuerten Immunantwort reagieren. Um diese Hypothese zu untersuchen, wurde eine umfangreiche in-silico Pipeline zur Vorhersage von potenziellen kreuzreaktiven T-Zell Epitoppaaren entwickelt. Diese berücksichtigt sowohl die MHC Bindungsaffinität, als auch die Sequenzähnlichkeit von den T-Zell Epitopen. Ein zusätzliches Bewertungssystem charakterisierte und priorisierte das Allergengegenstück basierend auf klinischer Relevanz. Die MHC Bindung der vorhergesagten Maus Balb/c MHC Klasse I Epitoppaare wurde in einem in-vitro Experiment validiert und positive Bindungspaare wurden für fortfolgende ex-vivo und in-vivo Analysen verwendet. Mit Hilfe von ex-vivo Stimulationsversuchen in einem RSV Mausmodell konnten Immunogenität der vorhergesagten Viruspeptide, sowie Kreuzreaktivität der korrespondierenden Allergenpeptide in Lungen- und Milzzellen bestätigt werden. Zusätzlich zeigte eine duale Pentamer-Färbung mit dem vorhergesagten Kandidatenpaar RSV A2 L356-364 FYNSMLNNI/Asp f 4192-200 WYGNSALTI virus- und allergenspezifische sowie doppelt positive CD8+ T-Effektor-Gedächtniszellen in Lungenzellen von RSV-infizierten Mäusen. Basierend auf diesem Ergebnis und der Tatsache, dass mehrere vorhergesagte Kandidatenpaare von Aspergillus fumigatus (Asp f) stammen, wurden Mäuse mit einem Pool von RSV A2 stammenden Peptiden immunisiert, von denen vorhergesagt wurde, dass sie mit von Asp f stammenden Peptiden kreuzreagieren. Die ex-vivo Stimulation von Milzzellen mit den vorhergesagten Allergenpeptiden führte zu einer erhöhten Proliferation, Aktivierung und Zytokinproduktion von CD8+ T-Zellen. Daraufhin wurde ein potenziell protektiver Effekt einer RSV A2 Infektion auf die Entwicklung von Asp f-induziertem experimentellem Asthma untersucht. Eine vorrangehende Virusinfektion führte zu weniger Eosinophilen und T2-assoziierten Zytokinen in der BAL in allergisch asthmatischen Mäusen im Vergleich zu solchen ohne Virusinfektion, sowie einem Trend für eine reduzierte Häufigkeit von Neutrophilen und T2-assozierten CD8+ T-Zellen in der Lunge. Des Weiteren konnte in Lungenhistologie-Schnitten eine verringerte Anzahl an Schleim-produzierende Becherzellen und weniger Entzündung detektiert werden. Um den Einfluss der vorhergesagten kreuzreaktiven T-Zell-Epitope zur Abschwächung der allergischen Reaktion zu untersuchen, wurden Mäuse mit den vorhergesagten, von RSV stammenden Peptiden immunisiert und anschließend dem Asp f-Mausmodell unterzogen. Diese Tiere wiesen im Vergleich zu Mäusen mit allergischem Asthma ohne vorherige Peptidimmunisierung eine geringere Anzahl an Eosinophilen in der BAL auf, sowie eine leichte Verringerung von IL-5+ CD8+ T Zellen und einer erhöhten Häufigkeit von IFNγ+ CD8+ T-Zellen in Lungenzellen. Neben RSV A2 wurden Epitoppaare für die Virusstämme des saisonalen quadrivalenten Influenza-Impfstoffs 2019/2020 (QIV) vorhergesagt und in-vitro validiert. Ein Mausmodell der Influenza-Impfung wurde etabliert, welches sowohl eine Antikörperantwort als auch eine virusspezifische T-Zell-Antwort induziert. Eine ex-vivo Stimulation von Milzzellen mit den vorhergesagten Allergenpeptiden führte zu einer erhöhten relativen Häufigkeit aktivierter CD8+ CD69+ T-Zellen im Vergleich zu dem Kontrollstimulus in QIV immunisierten Mäusen und nicht-immunisierten Tieren. Anschließend wurde die QIV-Immunisierung mit einem HDM-induzierten experimentellen Asthmamodell kombiniert und eine Reduktion verschiedener Merkmale von allergischem Asthma wurde hier ähnlich wie in dem RSV/Asp f Modell beobachtet, einschließlich der Anzahl von Eosinophilen, Lungenentzündung und Schleimproduktion. Zusammenfassend bestätigen diese Daten eine virusinduzierte heterologe Immunantworten auf Umweltallergene, die zu einer Abschwächung des Allergen-vermittelten experimentellen Asthmas führen. Dabei spielen mehrere epidemiologisch relevante respiratorische RNA-Viren eine Rolle. Ein erweiterter Virus-Peptidpool könnte erforderlich sein, um den gleichen Grad an Reduktion des allergischen Asthmas mit einer Peptid-Immunisierung gegenüber einer Virusinfektion zu induzieren. Weitere Experimente mit menschlichem Biomaterial zur Untersuchung kreuzreaktiver T-Zell-Populationen bei Asthmatikern und gesunden Personen, mit oder ohne Influenza Impfung, oder nach spezifischen Virusinfektionen, würden das translationale Potenzial unserer Ergebnisse unterstützen. Beweise in dieser Hinsicht könnten wichtige Implikationen für zukünftige Impfstrategien mit Peptiden haben, welche eine doppelte anti-virale und anti-allergische Antwort induzieren