Comprehensive Review of Human Plasmodium falciparum-Specific CD8+ T Cell Epitopes

Pathogenetic mechanisms and treatment targets in cerebral malaria

Malaria, the most prevalent mosquito-borne infectious disease worldwide, has accompanied humanity for millennia and remains an important public health issue despite advances in its prevention and treatment. Most infections are asymptomatic, but a small percentage of individuals with a heavy parasite burden develop severe malaria, a group of clinical syndromes attributable to organ dysfunction. Cerebral malaria is an infrequent but life-threatening complication of severe malaria that presents as an acute cerebrovascular encephalopathy characterized by unarousable coma. Despite effective antiparasite drug treatment, 20% of patients with cerebral malaria die from this disease, and many survivors of cerebral malaria have neurocognitive impairment. Thus, an important unmet clinical need is to rapidly identify people with malaria who are at risk of developing cerebral malaria and to develop preventive, adjunctive and neuroprotective treatments for cerebral malaria. This Review describes important advances in the understanding of cerebral malaria over the past two decades and discusses how these mechanistic insights could be translated into new therapies.

mRNA vaccine against malaria tailored for liver-resident memory T cells

Malaria is caused by Plasmodium species transmitted by Anopheles mosquitoes. Following a mosquito bite, Plasmodium sporozoites migrate from skin to liver, where extensive replication occurs, emerging later as merozoites that can infect red blood cells and cause symptoms of disease. As liver tissue-resident memory T cells (Trm cells) have recently been shown to control liver-stage infections, we embarked on a messenger RNA (mRNA)-based vaccine strategy to induce liver Trm cells to prevent malaria. Although a standard mRNA vaccine was unable to generate liver Trm or protect against challenge with Plasmodium berghei sporozoites in mice, addition of an agonist that recruits T cell help from type I natural killer T cells under mRNA-vaccination conditions resulted in significant generation of liver Trm cells and effective protection. Moreover, whereas previous exposure of mice to blood-stage infection impaired traditional vaccines based on attenuated sporozoites, mRNA vaccination was unaffected, underlining the potential for such a rational mRNA-based strategy in malaria-endemic regions.

Malaria vaccines

INTRODUCTION

: Eradication of malaria remains one of the main aims of medicine. Despite progress in malaria treatment, mortality rate remains high, especially in the poorest parts of the world. Therefore, prevention through vaccines is fundamental and recent approval of the first effective vaccine reinforced this assumption. However, since the parasite cycle is complex, being composed of three stages, different types of vaccine targeting stage-specific antigens shall be developed. Moreover, the beneficial effect on vaccinated subjects can be tuned using compositions targeting different disease stages.

AREA COVERED

: We analysed the malaria vaccine patent landscape describing the most significant patents published after 2016, classified according to the different parasite stages targeted focusing on selected protein antigens or epitopes. We searched "malaria vaccine" on Patentscope and Espacenet.

EXPERT OPINION

: Pre-erythrocytic vaccines were boosted by RTS,S approval, but its partial efficacy, limited to sporozoites, calls for compositions active against other disease stages. In particular, multi-antigens vaccines could be more effective than single-stage ones, as they would activate an immune response more similar to that acquired in endemic regions. Furthermore, vaccine storage is another factor to be taken into account given the climate of the areas where malaria is widespread. More advanced technologies can lead to more effective and safer vaccines.

Advances and challenges in automated malaria diagnosis using digital microscopy imaging with artificial intelligence tools: A review

Malaria is an infectious disease caused by parasites of the genus Plasmodium spp. It is transmitted to humans by the bite of an infected female Anopheles mosquito. It is the most common disease in resource-poor settings, with 241 million malaria cases reported in 2020 according to the World Health Organization. Optical microscopy examination of blood smears is the gold standard technique for malaria diagnosis; however, it is a time-consuming method and a well-trained microscopist is needed to perform the microbiological diagnosis. New techniques based on digital imaging analysis by deep learning and artificial intelligence methods are a challenging alternative tool for the diagnosis of infectious diseases. In particular, systems based on Convolutional Neural Networks for image detection of the malaria parasites emulate the microscopy visualization of an expert. Microscope automation provides a fast and low-cost diagnosis, requiring less supervision. Smartphones are a suitable option for microscopic diagnosis, allowing image capture and software identification of parasites. In addition, image analysis techniques could be a fast and optimal solution for the diagnosis of malaria, tuberculosis, or Neglected Tropical Diseases in endemic areas with low resources. The implementation of automated diagnosis by using smartphone applications and new digital imaging technologies in low-income areas is a challenge to achieve. Moreover, automating the movement of the microscope slide and image autofocusing of the samples by hardware implementation would systemize the procedure. These new diagnostic tools would join the global effort to fight against pandemic malaria and other infectious and poverty-related diseases.

Computational Clues of Immunogenic Hotspots in Plasmodium falciparum Erythrocytic Stage Vaccine Candidate Antigens: In Silico Approach

Malaria is the most pernicious parasitic infection, and Plasmodium falciparum is the most virulent species with substantial morbidity and mortality worldwide. The present in silico investigation was performed to reveal the biophysical characteristics and immunogenic epitopes of the 14 blood-stage proteins of the P. falciparum using comprehensive immunoinformatics approaches. For this aim, various web servers were employed to predict subcellular localization, antigenicity, allergenicity, solubility, physicochemical properties, posttranslational modification sites (PTMs), the presence of signal peptide, and transmembrane domains. Moreover, structural analysis for secondary and 3D model predictions were performed for all and stable proteins, respectively. Finally, human helper T lymphocyte (HTL) epitopes were predicted using HLA reference set of IEDB server and screened in terms of antigenicity, allergenicity, and IFN-γ induction as well as population coverage. Also, a multiserver B-cell epitope prediction was done with subsequent screening for antigenicity, allergenicity, and solubility. Altogether, these proteins showed appropriate antigenicity, abundant PTMs, and many B-cell and HTL epitopes, which could be directed for future vaccination studies in the context of multiepitope vaccine design.

CD8TCEI-EukPath: A Novel Predictor to Rapidly Identify CD8+ T-Cell Epitopes of Eukaryotic Pathogens Using a Hybrid Feature Selection Approach

Computational prediction to screen potential vaccine candidates has been proven to be a reliable way to provide guarantees for vaccine discovery in infectious diseases. As an important class of organisms causing infectious diseases, pathogenic eukaryotes (such as parasitic protozoans) have evolved the ability to colonize a wide range of hosts, including humans and animals; meanwhile, protective vaccines are urgently needed. Inspired by the immunological idea that pathogen-derived epitopes are able to mediate the CD8⁺ T-cell-related host adaptive immune response and with the available positive and negative CD8⁺ T-cell epitopes (TCEs), we proposed a novel predictor called CD8TCEI-EukPath to detect CD8⁺ TCEs of eukaryotic pathogens. Our method integrated multiple amino acid sequence-based hybrid features, employed a well-established feature selection technique, and eventually built an efficient machine learning classifier to differentiate CD8⁺ TCEs from non-CD8⁺ TCEs. Based on the feature selection results, 520 optimal hybrid features were used for modeling by utilizing the LightGBM algorithm. CD8TCEI-EukPath achieved impressive performance, with an accuracy of 79.255% in ten-fold cross-validation and an accuracy of 78.169% in the independent test. Collectively, CD8TCEI-EukPath will contribute to rapidly screening epitope-based vaccine candidates, particularly from large peptide-coding datasets. To conduct the prediction of CD8⁺ TCEs conveniently, an online web server is freely accessible (http://lab.malab.cn/∼hrs/CD8TCEI-EukPath/).

Genetic Diversity and Population Genetic Analysis of Plasmodium falciparum Thrombospondin Related Anonymous Protein (TRAP) in Clinical Samples from Saudi Arabia

The thrombospondin related anonymous protein (TRAP) is considered one of the most important pre-erythrocytic vaccine targets. Earlier population genetic studies revealed the TRAP gene to be under strong balancing natural selection. This study is the first attempt to analyze genetic diversity, natural selection, phylogeography and population structure in 199 clinical samples from Saudi Arabia using the full-length PfTRAP gene. We found the rate of nonsynonymous substitutions to be significantly higher than that of synonymous substitutions in the clinical samples, indicating a strong positive or diversifying selection for the full-length gene and the Von Willebrand factor (VWF). The nucleotide diversity was found to be π~0.00789 for the full-length gene; however, higher nucleotide diversity was observed for the VWF compared to the thrombospondin repeat region (TSP). Deduction of the amino acid sequence alignment of the PNP repeat region in the Saudi samples revealed six genotypes characterized by tripeptide repeat motifs (PNP, ANP, ENP and SNP). Haplotype network, population structure and population differentiation analyses indicated four distinct sub-populations in spite of the low geographical distance between the sampling sites. Our results suggest the likeliness of independent parasite evolution, creating opportunities for further adaptation, including host transition, and making malaria control even more challenging.

Dihydroartemisinin beneficially regulates splenic immune cell heterogeneity through the SOD3-JNK-AP-1 axis

The immunomodulatory potential of dihydroartemisinin (DHA) has recently been highlighted; however, the potential mechanism remains to be clarified. Single-cell RNA sequencing was explored in combination with cellular and biochemical approaches to elucidate the immunomodulatory mechanisms of DHA. In this study, we found that DHA induced both spleen enlargement and rearrangement of splenic immune cell subsets in mice. It was revealed that DHA promoted the reversible expansion of effective regulatory T cells and interferon-γ⁺ cytotoxic CD8⁺ T cells in the spleen via induction of superoxide dismutase 3 (SOD3) expression and increased phosphorylation of c-Jun N-terminal kinases (JNK) and its downstream activator protein 1 (AP-1) transcription factors. Further, SOD3 knockout mice were resistant to the regulatory effect of DHA. Thus, DHA, through the activation of the SOD3-JNK-AP-1 axis, beneficially regulated immune cell heterogeneity and splenic immune cell homeostasis to treat autoimmune diseases.

Bacillus subtilis spores as delivery system for nasal Plasmodium falciparum circumsporozoite surface protein immunization in a murine model

Malaria remains a widespread public health problem in tropical and subtropical regions around the world, and there is still no vaccine available for full protection. In recent years, it has been observed that spores of Bacillus subtillis can act as a vaccine carrier and adjuvant, promoting an elevated humoral response after co-administration with antigens either coupled or integrated to their surface. In our study, B. subtillis spores from the KO7 strain were used to couple the recombinant CSP protein of P. falciparum (rPfCSP), and the nasal humoral-induced immune response in Balb/C mice was evaluated. Our results demonstrate that the spores coupled to rPfCSP increase the immunogenicity of the antigen, which induces high levels of serum IgG, and with balanced Th1/Th2 immune response, being detected antibodies in serum samples for 250 days. Therefore, the use of B. subtilis spores appears to be promising for use as an adjuvant in a vaccine formulation.

Deciphering the Plasmodium falciparum malaria-specific CD4+ T-cell response: ex vivo detection of high frequencies of PD-1+TIGIT+ EXP1-specific CD4+ T cells using a novel HLA-DR11-restricted MHC class II tetramer

Relatively little is known about the ex vivo frequency and phenotype of the Plasmodium falciparum-specific CD4+ T-cell response in humans. The exported protein 1 (EXP1) is expressed by plasmodia at both, the liver stage and blood stage, of infection making it a potential target for CD4+ and CD8+ effector T cells. Here, a fluorochrome-labelled HLA-DRB1∗11:01-restriced MHC class II tetramer derived from the P. falciparum EXP1 (aa62-74) was established for ex vivo tetramer analysis and magnetic bead enrichment in 10 patients with acute malaria. EXP1-specific CD4+ T cells were detectable in 9 out of 10 (90%) malaria patients expressing the HLA-DRB1∗11 molecule with an average ex vivo frequency of 0.11% (0-0.22%) of total CD4+ T cells. The phenotype of EXP1-specific CD4+ T cells was further assessed using co-staining with activation (CD38, HLA-DR, CD26), differentiation (CD45RO, CCR7, KLRG1, CD127), senescence (CD57), and co-inhibitory (PD-1, TIGIT, LAG-3, TIM-3) markers as well as the ectonucleotidases CD39 and CD73. EXP1-specific tetramer+ CD4+ T cells had a distinct phenotype compared to bulk CD4+ T cells and displayed a highly activated effector memory phenotype with elevated levels of co-inhibitory receptors and activation markers: EXP1-specific CD4+ T cells universally expressed the co-inhibitory receptors PD-1 and TIGIT as well as the activation marker CD38 and showed elevated frequencies of CD39. These results demonstrate that MHC class II tetramer enrichment is a sensitive approach to investigate ex vivo antigen-specific CD4+ T cells in malaria patients that will aid further analysis of the role of CD4+ T cells during malaria.

In silico analysis and prediction of immunogenic epitopes for pre-erythrocytic proteins of the deadly Plasmodium falciparum

Malaria is the deadliest parasitic disease in tropical and subtropical areas around the world, with considerable morbidity and mortality, particularly due to the life-threatening Plasmodium falciparum. The present in silico investigation was performed to reveal the biophysical characteristics and immunogenic epitopes of the six pre-erythrocytic proteins of the P. falciparum using comprehensive immunoinformatics approaches. For this aim, different web servers were employed to predict subcellular localization, antigenicity, allergenicity, solubility, physico-chemical properties, post-translational modification sites (PTMs), the presence of signal peptide and transmembrane domains. Moreover, the secondary and tertiary structures of the proteins were revealed followed by refinement and validations. Finally, NetCTL server was used to predict cytotoxic T-lymphocyte (CTL) epitopes, followed by subsequent screening in terms of antigenicity and immunogenicity. Also, IEDB server was utilized to predict helper T-lymphocyte (HTL) epitopes, followed by screening regarding interferon gamma induction and population coverage. These proteins showed appropriate antigenicity, abundant PTMs as well as many CTL and HTL epitopes, which could be directed for future vaccination studies in the context of multi-epitope vaccine design.

A guide to investigating immune responses elicited by whole-sporozoite pre-erythrocytic vaccines against malaria

In the last few decades, considerable efforts have been made toward the development of efficient vaccines against malaria. Whole-sporozoite (Wsp) vaccines, which induce efficient immune responses against the pre-erythrocytic (PE) stages (sporozoites and liver forms) of Plasmodium parasites, the causative agents of malaria, are among the most promising immunization strategies tested until present. Several Wsp PE vaccination approaches are currently under evaluation in the clinic, including radiation- or genetically-attenuated Plasmodium sporozoites, live parasites combined with chemoprophylaxis, or genetically modified rodent Plasmodium parasites. In addition to the assessment of their protective efficacy, clinical trials of Wsp PE vaccine candidates inevitably involve the thorough investigation of the immune responses elicited by vaccination, as well as the identification of correlates of protection. Here, we review the main methodologies employed to dissect the humoral and cellular immune responses observed in the context of Wsp PE vaccine clinical trials and discuss future strategies to further deepen the knowledge generated by these studies, providing a toolbox for the in-depth analysis of vaccine-induced immunogenicity.

Benchmarking Datasets from Malaria Cytotoxic T-cell Epitopes Using Machine Learning Approach

Background:

Epitope prediction remains a major challenge in malaria due to the unique parasite biology, in addition to rapidly evolving parasite sequence variation in Plasmodium species. Although several models for epitope prediction exist, they are not useful in Plasmodium specific epitope development. Hence, it was proposed to use machine learning based methods to develop a peptide sequence based epitope predictor specific for malaria.

Methods:

Model datasets were developed and performance was tested using various machine learning algorithms. Machine learning classifiers were trained on epitope data using sequence features and comparison of amino acid physicochemical properties was done to yield a valid prediction model.

Results:

The findings from the analysis reveal that the model developed using selected classifiers after preprocessing by Waikato Environment for Knowledge Analysis (WEKA) performed better than other methods. The datasets for benchmarks of performance are deposited in the repository https://github.com/githubramaadiga/epitope_dataset .

Conclusion:

The study is the first in-silico study on benchmarking Plasmodium cytotoxic T cell epitope datasets using machine learning approach. The peptide based predictors have been used for the first time to classify cytotoxic T cell epitopes in malaria. Algorithms has been evaluated using real datasets from malaria to obtain the model.

SARS-CoV-2 and Plasmodium falciparum common immunodominant regions may explain low COVID-19 incidence in the malaria-endemic belt

Coronavirus disease 2019 (COVID-19) has caused significant morbidity and mortality and new cases are on the rise globally, yet malaria-endemic areas report statistically significant lower incidences. We identified potential shared targets for an immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by immune determinants' shared identities with P. falciparum using the Immune Epitope Database and Analysis Resource Immune 9.0 browser tool. Probable cross-reactivity is suggested through HLA-A∗02:01 and subsequent CD8+ T-cell activation. The apparent immunodominant epitope conservation between SARS-CoV-2 (N and open reading frame (ORF) 1ab) and P. falciparum thrombospondin-related anonymous protein (TRAP) may underlie the low COVID-19 incidence in the malaria-endemic zone by providing immunity against virus infection to those previously infected with Plasmodium. Additionally, we hypothesize that the shared epitopes which lie within antigens that aid in the establishment of the P. falciparum erythrocyte invasion may be an alternative route for SARS-CoV-2 via the erythrocyte CD147 receptor, although this remains to be proven.

Plasmodium sporozoites induce regulatory macrophages

Professional antigen-presenting cells (APCs), like macrophages (Mϕs) and dendritic cells (DCs), are central players in the induction of natural and vaccine-induced immunity to malaria, yet very little is known about the interaction of SPZ with human APCs. Intradermal delivery of whole-sporozoite vaccines reduces their effectivity, possibly due to dermal immunoregulatory effects. Therefore, understanding these interactions could prove pivotal to malaria vaccination. We investigated human APC responses to recombinant circumsporozoite protein (recCSP), SPZ and anti-CSP opsonized SPZ both in monocyte derived MoDCs and MoMϕs. Both MoDCs and MoMϕs readily took up recCSP but did not change phenotype or function upon doing so. SPZ are preferentially phagocytosed by MoMϕs instead of DCs and phagocytosis greatly increased after opsonization. Subsequently MoMϕs show increased surface marker expression of activation markers as well as tolerogenic markers such as Programmed Death-Ligand 1 (PD-L1). Additionally they show reduced motility, produce interleukin 10 and suppressed interferon gamma (IFNγ) production by antigen specific CD8⁺ T cells. Importantly, we investigated phenotypic responses to SPZ in primary dermal APCs isolated from human skin explants, which respond similarly to their monocyte-derived counterparts. These findings are a first step in enhancing our understanding of pre-erythrocytic natural immunity and the pitfalls of intradermal vaccination-induced immunity.

Malaria continues to be the deadliest parasitic disease worldwide, and an effective vaccine yielding sterile immunity does not yet exist. Attenuated parasites can induce sterile protection in both human and rodent models for malaria, but these vaccines need to be administered directly into the bloodstream in order to convey protection; administration via the skin results in a much-reduced efficacy. We hypothesized this is caused by an early immune regulation initiated at the first site of contact with the immune system: the skin. However, the human skin stage of malaria has not been investigated to date. We used human antigen presenting cells as well as whole human skin explants to investigate (dermal) immune responses and found that Plasmodium sporozoites are able to suppress immune responses by inducing regulatory macrophages. Our study provides new insights in the mechanism of early immune regulation exploited by Plasmodium parasites and can help to explain why intradermal vaccination using whole attenuated sporozoites results in reduced protection.

Detection of EXP1-Specific CD4+ T Cell Responses Directed Against a Broad Range of Epitopes Including Two Promiscuous MHC Class II Binders During Acute Plasmodium falciparum Malaria

Background: T cells are thought to play a major role in conferring immunity against malaria. This study aimed to comprehensively define the breadth and specificity of the Plasmodium falciparum (P. falciparum)-specific CD4+ T cell response directed against the exported protein 1 (EXP1) in a cohort of patients diagnosed with acute malaria.

Methods: Peripheral blood mononuclear cells of 44 patients acutely infected with P. falciparum, and of one patient infected with P. vivax, were stimulated and cultured in vitro with an overlapping set of 31 P. falciparum-specific 13-17-mer peptides covering the entire EXP1 sequence. EXP1-specific T cell responses were analyzed by ELISPOT and intracellular cytokine staining for interferon-γ production after re-stimulation with individual peptides. For further characterization of the epitopes, in silico and in vitro human leukocyte antigen (HLA) binding studies and fine mapping assays were performed.

Results: We detected one or more EXP1-specific CD4+ T cell responses (mean: 1.09, range 0–5) in 47% (21/45) of our patients. Responses were directed against 15 of the 31 EXP1 peptides. Peptides EXP1-P13 (aa60-74) and P15 (aa70-85) were detected by 18% (n = 8) and 27% (n = 12) of the 45 patients screened. The optimal length, as well as the corresponding most likely HLA-restriction, of each of these two peptides was assessed. Interestingly, we also identified one CD4+ T cell response against peptide EXP1-P15 in a patient who was infected with P. vivax but not falciparum.

Conclusions: This first detailed characterization of novel EXP1-specific T cell epitopes provides important information for future analysis with major histocompatibility complex-multimer technology as well as for immunomonitoring and vaccine design.

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

BACKGROUND

Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have been shown to provide significant protection against controlled human malaria infection (CHMI) in clinical trials. Initial CHMI studies showed significantly higher durable protection against homologous than heterologous strains, suggesting the presence of strain-specific vaccine-induced protection. However, interpretation of these results and understanding of their relevance to vaccine efficacy have been hampered by the lack of knowledge on genetic differences between vaccine and CHMI strains, and how these strains are related to parasites in malaria endemic regions.

METHODS

Whole genome sequencing using long-read (Pacific Biosciences) and short-read (Illumina) sequencing platforms was conducted to generate de novo genome assemblies for the vaccine strain, NF54, and for strains used in heterologous CHMI (7G8 from Brazil, NF166.C8 from Guinea, and NF135.C10 from Cambodia). The assemblies were used to characterize sequences in each strain relative to the reference 3D7 (a clone of NF54) genome. Strains were compared to each other and to a collection of clinical isolates (sequenced as part of this study or from public repositories) from South America, sub-Saharan Africa, and Southeast Asia.

RESULTS

While few variants were detected between 3D7 and NF54, we identified tens of thousands of variants between NF54 and the three heterologous strains. These variants include SNPs, indels, and small structural variants that fall in regulatory and immunologically important regions, including transcription factors (such as PfAP2-L and PfAP2-G) and pre-erythrocytic antigens that may be key for sporozoite vaccine-induced protection. Additionally, these variants directly contributed to diversity in immunologically important regions of the genomes as detected through in silico CD8+ T cell epitope predictions. Of all heterologous strains, NF135.C10 had the highest number of unique predicted epitope sequences when compared to NF54. Comparison to global clinical isolates revealed that these four strains are representative of their geographic origin despite long-term culture adaptation; of note, NF135.C10 is from an admixed population, and not part of recently formed subpopulations resistant to artemisinin-based therapies present in the Greater Mekong Sub-region.

CONCLUSIONS

These results will assist in the interpretation of vaccine efficacy of whole-organism vaccines against homologous and heterologous CHMI.

Using two phases of the CD4 T cell response to blood-stage murine malaria to understand regulation of systemic immunity and placental pathology in Plasmodium falciparum infection

Plasmodium falciparum infection and malaria remain a risk for millions of children and pregnant women. Here, we seek to integrate knowledge of mouse and human T helper cell (Th) responses to blood-stage Plasmodium infection to understand their contribution to protection and pathology. Although there is no complete Th subset differentiation, the adaptive response occurs in two phases in non-lethal rodent Plasmodium infection, coordinated by Th cells. In short, cellular immune responses limit the peak of parasitemia during the first phase; in the second phase, humoral immunity from T cell-dependent germinal centers is critical for complete clearance of rapidly changing parasite. A strong IFN-γ response kills parasite, but an excess of TNF compared with regulatory cytokines (IL-10, TGF-β) can cause immunopathology. This common pathway for pathology is associated with anemia, cerebral malaria, and placental malaria. These two phases can be used to both understand how the host responds to rapidly growing parasite and how it attempts to control immunopathology and variation. This dual nature of T cell immunity to Plasmodium is discussed, with particular reference to the protective nature of the continuous generation of effector T cells, and the unique contribution of effector memory T cells.