A state-of-the-art methodology for high-throughput in silico vaccine discovery against protozoan parasites and exemplified with discovered candidates for Toxoplasma gondii

Genome of the invasive North American Haemaphysalis longicornis tick as a template for bovine anti-tick vaccine discovery

BACKGROUND

The ixodid tick Haemaphysalis longicornis Neumann, commonly referred to as the Asian longhorned tick, has expanded its range outside of East Asia into countries such as Australia, New Zealand, and the United States. Since the first U.S. detection in 2017, H. longicornis has spread to 21 states and the District of Columbia and has been implicated as a vector of various human and animal pathogens including Theileria orientalis Ikeda genotype, a causal agent of bovine theileriosis. Facilitated in part by the parthenogenetic nature of invasive populations, this tick has become a paramount threat to agricultural rangelands and U.S. livestock production. Reliance on traditional acaricides for vector control selects for resistant individuals, reducing the effectiveness of many chemical tools over time. Thus, focus has shifted to alternative control mechanisms including anti-tick vaccine development. To further such research, here we sequence and assemble a high-quality H. longicornis genome and robust gene catalog from invasive North American ticks while also providing an organ-specific transcriptomic expression catalog and in-depth informatic screening of the tick proteome for potential bovine antigenic molecules with potential utility as vaccine candidates.

RESULTS

Using a combination of PacBio HiFi single-molecule sequencing and Hi-C chromosome conformation capture data, our genome assembly contains 270 scaffolds and spans a haploid genome size of 3.09 Gbp with an N50 of 213.4 Mbp. Gene prediction identified 21,947 high-confidence gene structures containing 96.2% of the core Arthropoda odb10 orthologs. Our organ-specific transcriptome library comprising salivary glands, midgut, ovaries, foreleg and hindleg additionally highlights potential anti-tick vaccine candidates and metabolic pathways to target for future in vitro trials.

CONCLUSIONS

Single-molecule sequencing of a triploid, parthenogenetic North American Haemaphysalis longicornis tick allowed for the generation of a highly contiguous genome assembly that, when coupled with extensive transcriptome profiling, resulted in a robust gene catalog containing multiple candidates for further study as anti-tick vaccine antigens.

Chemical and biological investigations on modified gemcitabine by nanoliposome structured on cholesterol, pectin, and phosphatidylcholine as an anticancer drug via a drug delivery system

Gemcitabine hydrochloride (GEM) mimics one of the building blocks of DNA and RNA, so it indicates possible chemotherapeutic effects. It prevents cancer cells from producing DNA and proteins, which ultimately leads to their death. The goal of this work is to modify the GEM medication by nanoforming nanoliposomes based on the composition of Cholesterol, pectin nanoparticles, and phosphatidylcholine (PhC). The drug in nanoliposome form is made using the precipitation method, and several approaches are employed to characterize it. UV-Vis spectroscopy is used to measure the release process of GEM from the lipids and its integration with them. Results of the combination efficiency for PhC.Pectin@GEM, PhC.GEM@Pectin, and PhC@Cholestrol.GEM were recorded at 78.8 %, 83 %, and 80 %, respectively. A UV-Vis spectrophotometer was used to determine the release efficiency of the nanoliposomes, which was measured at pH values of 3, 6.8, and 7.4. The in-vitro investigation employed SRB (Routine analysis IC50) to determine the modified drug's toxicity on breast adenocarcinoma (MCF-7) cells, while the in-vitro study assessed the produced nanoliposomes' capacity to do so. The conclusion is that to ascertain whether GEM medicine's nanoliposomes can effectively treat breast cancer in place of GEM medication, clinical trials are necessary to prove the ability for treatment.

In silico identification and ex vivo evaluation of Toxoplasma gondii peptides restricted to HLA-A*02, HLA-A*24 and HLA-B*35 alleles in human PBMC from a Colombian population

Toxoplasma gondii infects approximately 30% of the population, and there is currently no approved vaccine. Identifying immunogenic peptides with high affinity to different HLA molecules is a promising vaccine strategy. This study used an in silico approach using artificial neural networks to identify T. gondii peptides restricted to HLA-A*02, HLA-A*24, and HLA-B*35 alleles. Proteomes from seven T. gondii strains and transcriptomic data of overexpressed genes from T. gondii-RH in human PBMC were also used. Parasite protein sequences were analyzed with R 'Epitope Prediction' library. Peptide candidates were evaluated in the artificial neural networks based on the probabilities of output neurons (p > 0.5). The IFN-γ responses in PBMC from T. gondii seronegative and seropositive individuals were evaluated by ELISpot. Peptides with higher IFN-γ induction were evaluated to identify cytotoxic response in CD8+ T cells (CD107a). In silico analysis identified 36 peptides from T. gondii proteins with predicted affinity to HLA-A*02, A*24, and B*35 alleles. Experiments with PBMCs revealed that a peptide restricted to HLA-A02 (P1: FLFAWITYV) induced a significant increase in IFN-γ-producing cells (p = 0.004). For HLA-A24, a peptide (P8: VFAFAFAFFLI) also induced a significant IFN-γ response (p = 0.004), while for the HLA-B*35 allele, the P6 peptide (YPIAPSFAM) induced a response that differed significantly from the control (p = 0.05). These peptides induced also a significant percentage of central memory CD8 + T cells expressing the degranulation marker CD107a (p < 0.05). Finally, we identified three T. gondii peptides that induced IFN-γ response, and a cytotoxic response measured by CD107a expression on CD45RAneg-CD8 cells. These peptides could be considered part of a multi-epitope vaccine against toxoplasmosis in humans.

Resequencing and characterization of the first Corynebacterium pseudotuberculosis genome isolated from camel

Background

Corynebacterium pseudotuberculosis is a zoonotic Gram-positive bacterial pathogen known to cause different diseases in many mammals, including lymph node abscesses in camels. Strains from biovars equi and ovis of C. pseudotuberculosis can infect camels. Comparative genomics could help to identify features related to host adaptation, and currently strain Cp162 from biovar equi is the only one from camel with a sequenced genome.

Methods

In this work, we compared the quality of three genome assemblies of strain Cp162 that used data from the DNA sequencing platforms SOLiD v3 Plus, IonTorrent PGM, and Illumina HiSeq 2500 with an optical map and investigate the unique features of this strain. For this purpose, we applied comparative genomic analysis on the different Cp162 genome assembly versions and included other 129 genomes from the same species.

Results

Since the first version of the genome, there was an increase of 88 Kbp and 121 protein-coding sequences, a decrease of pseudogenes from 139 to 53, and two inversions and one rearrangement corrected. We identified 30 virulence genes, none associated to the camel host, and the genes rpob2 and rbpA predicted to confer resistance to rifampin. In comparison to 129 genomes of the same species, strain Cp162 has four genes exclusively present, two of them code transposases and two truncated proteins, and the three exclusively absent genes lysG, NUDIX domain protein, and Hypothetical protein. All 130 genomes had the rifampin resistance genes rpob2 and rbpA. Our results found no unique gene that could be associated with tropism to camel host, and further studies should include more genomes and genome-wide association studies testing for genes and SNPs.

Identification and prioritisation of potential vaccine candidates using subtractive proteomics and designing of a multi-epitope vaccine against Wuchereria bancrofti

This study employed subtractive proteomics and immunoinformatics to analyze the Wuchereria bancrofti proteome and identify potential therapeutic targets, with a focus on designing a vaccine against the parasite species. A comprehensive bioinformatics analysis of the parasite's proteome identified 51 probable therapeutic targets, among which "Kunitz/bovine pancreatic trypsin inhibitor domain-containing protein" was identified as the most promising vaccine candidate. The candidate protein was used to design a multi-epitope vaccine, incorporating B-cell and T-cell epitopes identified through various tools. The vaccine construct underwent extensive analysis of its antigenic, physical, and chemical features, including the determination of secondary and tertiary structures. Docking and molecular dynamics simulations were performed with HLA alleles, Toll-like receptor 4 (TLR4), and TLR3 to assess its potential to elicit the human immune response. Immune simulation analysis confirmed the predicted vaccine's strong binding affinity with immunoglobulins, indicating its potential efficacy in generating an immune response. However, experimental validation and testing of this multi-epitope vaccine construct would be needed to assess its potential against W. bancrofti and even for a broader range of lymphatic filarial infections given the similarities between W. bancrofti and Brugia.

Proteomics Applications in Toxoplasma gondii: Unveiling the Host-Parasite Interactions and Therapeutic Target Discovery

Toxoplasma gondii, a protozoan parasite with the ability to infect various warm-blooded vertebrates, including humans, is the causative agent of toxoplasmosis. This infection poses significant risks, leading to severe complications in immunocompromised individuals and potentially affecting the fetus through congenital transmission. A comprehensive understanding of the intricate molecular interactions between T. gondii and its host is pivotal for the development of effective therapeutic strategies. This review emphasizes the crucial role of proteomics in T. gondii research, with a specific focus on host-parasite interactions, post-translational modifications (PTMs), PTM crosstalk, and ongoing efforts in drug discovery. Additionally, we provide an overview of recent advancements in proteomics techniques, encompassing interactome sample preparation methods such as BioID (BirA*-mediated proximity-dependent biotin identification), APEX (ascorbate peroxidase-mediated proximity labeling), and Y2H (yeast two hybrid), as well as various proteomics approaches, including single-cell analysis, DIA (data-independent acquisition), targeted, top-down, and plasma proteomics. Furthermore, we discuss bioinformatics and the integration of proteomics with other omics technologies, highlighting its potential in unraveling the intricate mechanisms of T. gondii pathogenesis and identifying novel therapeutic targets.