ORFeome Phage Display

Zantow, Jonas; Moreira, Gustavo Marçal Schmidt Garcia; Dübel, Stefan; Hust, Michael

doi:10.1007/978-1-4939-7447-4_27

Cited by 10 publications

(7 citation statements)

References 22 publications

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“…In particular, peptide arrays are limited by the maximal length of the synthetic peptides (typically around 15-20 amino acids), thus missing conformational or many non-linear epitopes, which make up a significant fraction, i.e., around 40%, of antibody epitopes [32]. ORFeome display can detect immunogenic proteins independent of the transcriptome or proteome, as it does not rely on cDNA or protein extracts [33][34][35]. In this study, we present an ORFeome phage display approach with the aim of identifying immunogenic peptide sequences across the SARS-CoV-2 genome.…”

Section: Introductionmentioning

confidence: 99%

ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein

Ballmann

Hotop

Bertoglio

et al. 2022

Viruses

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The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of the spike, and therefore lose neutralization efficacy against emerging SARS-CoV-2 variants, which frequently mutate in the RBD region. Previously, phage display has been used to identify epitopes of antibody responses against several diseases. Such epitopes have been applied to design vaccines or neutralize antibodies. Here, we constructed an ORFeome phage display library for the SARS-CoV-2 genome. Open reading frames (ORFs) representing the SARS-CoV-2 genome were displayed on the surface of phage particles in order to identify enriched immunogenic epitopes from COVID-19 patients. Library quality was assessed by both NGS and epitope mapping of a monoclonal antibody with a known binding site. The most prominent epitope captured represented parts of the fusion peptide (FP) of the spike. It is associated with the cell entry mechanism of SARS-CoV-2 into the host cell; the serine protease TMPRSS2 cleaves the spike within this sequence. Blocking this mechanism could be a potential target for non-RBD binding therapeutic anti-SARS-CoV-2 antibodies. As mutations within the FP amino acid sequence have been rather rare among SARS-CoV-2 variants so far, this may provide an advantage in the fight against future virus variants.

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Section: Introductionmentioning

confidence: 99%

ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein

Ballmann

Hotop

Bertoglio

et al. 2022

Viruses

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“…Another application of phage display is for the display of entire ORFeomes and metagenomes. This technique, which employs a library built with antigen fragments from bacterial genomes, metagenomes, or cDNA, was described to allow the discovery of novel oligopeptide markers using sera or other sources of polyclonal antibodies 40,41,57,58 . Even though this ORFeome application could be used in the present study using polyclonal antibodies against Listeria, it would provide information about immunogenic proteins that are applicable for indirect detection.…”

Section: Discussionmentioning

confidence: 99%

“…Recombinant mAbs generated by phage display are currently a valuable resource for basic research, diagnostics, and therapeutic applications 33 – 37 . On the other hand, improvements in antigen phage display technology have been achieved due to the availability of Hyperphage 38 , such as ORFeome phage display 39 – 41 . This technology can be employed for the discovery of biomarkers, which then can be used for the development of vaccines and diagnostics.…”

Section: Introductionmentioning

confidence: 99%

Pyruvate dehydrogenase complex—enzyme 2, a new target for Listeria spp. detection identified using combined phage display technologies

Moreira

Köllner

Helmsing

et al. 2020

Sci Rep

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The genus Listeria comprises ubiquitous bacteria, commonly present in foods and food production facilities. In this study, three different phage display technologies were employed to discover targets, and to generate and characterize novel antibodies against Listeria: antibody display for biomarker discovery and antibody generation; ORFeome display for target identification; and single-gene display for epitope characterization. With this approach, pyruvate dehydrogenase complex—enzyme 2 (PDC-E2) was defined as a new detection target for Listeria, as confirmed by immunomagnetic separation-mass spectrometry (IMS-MS). Immunoblot and fluorescence microscopy showed that this protein is accessible on the bacterial cell surface of living cells. Recombinant PDC-E2 was produced in E. coli and used to generate 16 additional antibodies. The resulting set of 20 monoclonal scFv-Fc was tested in indirect ELISA against 17 Listeria and 16 non-Listeria species. Two of them provided 100% sensitivity (CI 82.35–100.0%) and specificity (CI 78.20–100.0%), confirming PDC-E2 as a suitable target for the detection of Listeria. The binding region of 18 of these antibodies was analyzed, revealing that ≈ 90% (16/18) bind to the lipoyl domains (LD) of the target. The novel target PDC-E2 and highly specific antibodies against it offer new opportunities to improve the detection of Listeria.

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“…This approach is biased by the fact that a priori knowledge of targets is not always possible and only those antibodies that bind to the tested antigens are identified. High-throughput screens of proteomes for antigens [19] or of random peptide libraries for peptidic epitopes [20] can identify immunogenic targets. Such functional analyses provide a more meaningful profile in the immunological sense and, if carried out from blood, it is less prone to sampling error than cell-based sequencing approaches.…”

Section: Introductionmentioning

confidence: 99%

Network Organization of Antibody Interactions in Sequence and Structure Space: the RADARS Model

Prechl¹

2020

Antibodies

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Adaptive immunity in vertebrates is a complex self-organizing network of molecular interactions. While deep sequencing of the immune-receptor repertoire may reveal clonal relationships, functional interpretation of such data is hampered by the inherent limitations of converting sequence to structure to function. In this paper, a novel model of antibody interaction space and network, termed radial adjustment of system resolution, RAdial ADjustment of System Resolution (RADARS), is proposed. The model is based on the radial growth of interaction affinity of antibodies towards an infinity of directions in structure space, each direction corresponding to particular shapes of antigen epitopes. Levels of interaction affinity appear as free energy shells of the system, where hierarchical B-cell development and differentiation takes place. Equilibrium in this immunological thermodynamic system can be described by a power law distribution of antibody-free energies with an ideal network degree exponent of phi square, representing a scale-free fractal network of antibody interactions. Plasma cells are network hubs, memory B cells are nodes with intermediate degrees, and B1 cells function as nodes with minimal degree. Overall, the RADARS model implies that a finite number of antibody structures can interact with an infinite number of antigens by immunologically controlled adjustment of interaction energy distribution. Understanding quantitative network properties of the system should help the organization of sequence-derived predicted structural data.

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ORFeome Phage Display

Cited by 10 publications

References 22 publications

ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein

ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein

Pyruvate dehydrogenase complex—enzyme 2, a new target for Listeria spp. detection identified using combined phage display technologies

Network Organization of Antibody Interactions in Sequence and Structure Space: the RADARS Model

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