APRANK: Computational Prioritization of Antigenic Proteins and Peptides From Complete Pathogen Proteomes

Ricci, Alejandro D; Brunner, Mauricio; Ramoa, Diego; Carmona, Santiago J.; Nielsen, Morten; Agüero, Fernán

doi:10.3389/fimmu.2021.702552

Cited by 7 publications

(5 citation statements)

References 49 publications

(63 reference statements)

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“…Due to the breadth and diversity of the clinical samples analysed, this study also provides a large set of experimentally validated negative data (non-antigenic proteins and peptides). This is almost always overlooked, but it represents a highly valuable dataset for the training of predictors, which often needs to work under the assumption that proteins with no previous information on their antigenicity are non-antigenic 54 , 55 . The datasets from the primary discovery screening also provide a large corpus of data on dominant T. cruzi peptides reactive to sera from healthy subjects from different human populations.…”

Section: Discussionmentioning

confidence: 99%

The Trypanosoma cruzi Antigen and Epitope Atlas: antibody specificities in Chagas disease patients across the Americas

et al. 2023

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During an infection the immune system produces pathogen-specific antibodies. These antibody repertoires become specific to the history of infections and represent a rich source of diagnostic markers. However, the specificities of these antibodies are mostly unknown. Here, using high-density peptide arrays we examined the human antibody repertoires of Chagas disease patients. Chagas disease is a neglected disease caused by Trypanosoma cruzi, a protozoan parasite that evades immune mediated elimination and mounts long-lasting chronic infections. We describe a proteome-wide search for antigens, characterised their linear epitopes, and show their reactivity on 71 individuals from diverse human populations. Using single-residue mutagenesis we revealed the core functional residues for 232 of these epitopes. Finally, we show the diagnostic performance of identified antigens on challenging samples. These datasets enable the study of the Chagas antibody repertoire at an unprecedented depth and granularity, while also providing a rich source of serological biomarkers.

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Section: Discussionmentioning

confidence: 99%

The Trypanosoma cruzi Antigen and Epitope Atlas: antibody specificities in Chagas disease patients across the Americas

et al. 2023

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“…BepiPred 1.0 was the most frequently used software. There are also other B-cell epitope prediction software’s like Antigenic Protein and Peptide Ranker (APRANK) ( https://github.com/trypanosomatics/aprank ) [ 31 ] and Epipred ( http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/epipred/ ) that were not included in this review.…”

Section: Resultsmentioning

confidence: 99%

Scoping review of the applications of peptide microarrays on the fight against human infections

et al. 2022

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Introduction This scoping review explores the use of peptide microarrays in the fight against infectious diseases. The research domains explored included the use of peptide microarrays in the mapping of linear B-cell and T cell epitopes, antimicrobial peptide discovery, immunosignature characterisation and disease immunodiagnostics. This review also provides a short overview of peptide microarray synthesis. Methods Electronic databases were systematically searched to identify relevant studies. The review was conducted using the Joanna Briggs Institute methodology for scoping reviews and data charting was performed using a predefined form. The results were reported by narrative synthesis in line with the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews guidelines. Results Ninety-five articles from 103 studies were included in the final data charting process. The majority (92. 0%) of the articles were published during 2010–2020 and were mostly from Europe (44.2%) and North America (34.7%). The findings were from the investigation of viral (45.6%), bacterial (32. 0%), parasitic (23.3%) and fungal (2. 0%) infections. Out of the serological studies, IgG was the most reported antibody type followed by IgM. The largest portion of the studies (77.7%) were related to mapping B-cell linear epitopes, 5.8% were on diagnostics, 5.8% reported on immunosignature characterisation and 8.7% reported on viral and bacterial cell binding assays. Two studies reported on T-cell epitope profiling. Conclusion The most important application of peptide microarrays was found to be B-cell epitope mapping or antibody profiling to identify diagnostic and vaccine targets. Immunosignatures identified by random peptide microarrays were found to be applied in the diagnosis of infections and interrogation of vaccine responses. The analysis of the interactions of random peptide microarrays with bacterial and viral cells using binding assays enabled the identification of antimicrobial peptides. Peptide microarray arrays were also used for T-cell linear epitope mapping which may provide more information for the design of peptide-based vaccines and for the development of diagnostic reagents.

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“…Therefore, we were interested to see retrospectively if our prioritization scheme would have been influenced by this and two other recently described methods. One is the 'Antigenic Protein and Peptide Ranker' (APRANK), aimed at prioritizing putative antigens of several pathogens, including T. gondii, based on in silico analyses (Ricci et al, 2021). The other is the recently improved BepiPred algorithm (V3) (Clifford et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Limited value of current and new in silico predicted oocyst-specific proteins of Toxoplasma gondii for source-attributing serology

López-Ureña,

Calero-Bernal,

Koudela

et al. 2023

Front. Parasitol.

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Toxoplasma gondii is a zoonotic parasite infecting all warm-blooded animals, including humans. The contribution of environmental contamination by T. gondii oocysts to infections is understudied. The aim of the current work was to explore T. gondii serology as a means of attributing the source of infection using a robust stepwise approach. We identified in silico thirty-two promising oocyst-specific antigens from T. gondii ´omics data, recombinantly expressed and purified them and validated whether serology based on these proteins could discriminate oocyst- from tissue cyst-driven experimental infections. For this, three well-characterized serum panels, sampled from 0 to 6 weeks post-infection, from pigs and sheep experimentally infected with T. gondii oocysts or tissue cysts, were used. Candidate proteins were initially screened by Western blot with sera from pigs or sheep, infected for different times, either with oocysts or tissue cysts, as well as non-infected animals. Only the recombinant proteins TgCCp5A and TgSR1 provoked seroconversion upon infection and appeared to discriminate between oocyst- and tissue cyst-driven infections with pig sera. They were subsequently used to develop an enzyme-linked immunosorbent assay test for pigs. Based on this assay and Western blot analyses, a lack of stage specificity and low antigenicity was observed with all pig sera. The same was true for proteins TgERP, TgSporoSAG, TgOWP1 and TgOWP8, previously described as source-attributing antigens, when analyzed using the whole panels of sera. We conclude that there is currently no antigen that allows the discrimination of T. gondii infections acquired from either oocysts or tissue cysts by serological tests. This work provides robust new knowledge that can inform further research and development toward source-attributing T. gondii serology.

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APRANK: Computational Prioritization of Antigenic Proteins and Peptides From Complete Pathogen Proteomes

Cited by 7 publications

References 49 publications

The Trypanosoma cruzi Antigen and Epitope Atlas: antibody specificities in Chagas disease patients across the Americas

The Trypanosoma cruzi Antigen and Epitope Atlas: antibody specificities in Chagas disease patients across the Americas

Scoping review of the applications of peptide microarrays on the fight against human infections

Limited value of current and new in silico predicted oocyst-specific proteins of Toxoplasma gondii for source-attributing serology

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