Bacteriophage vehicles for phage display: biology, mechanism, and application

Targeting breast cancer: the promise of phage-based nanomedicines

BACKGROUND

Breast cancer is a leading cause of cancer-related mortality among women worldwide, characterized by its aggressive nature, propensity for metastasis, and resistance to standard treatment modalities. Traditional therapies, including surgery, chemotherapy, and radiation, often encounter significant limitations such as systemic toxicity and lack of specificity.

OBJECTIVE

This review aims to evaluate the recent advancements in phage-based nanomedicines as a novel approach for targeted breast cancer therapy, focusing on their mechanisms of action, therapeutic benefits, and the challenges faced in clinical implementation.

METHODS

A comprehensive literature review was conducted, analyzing studies that investigate the application of bacteriophages in cancer therapy, particularly in breast cancer. The review highlights the integration of nanotechnology with phage therapy, examining the potential for enhanced targeting and reduced side effects.

RESULTS

Phage-based nanomedicines have shown promise in selectively targeting breast cancer cells while sparing healthy tissues, thereby improving therapeutic efficacy and safety profiles. The unique properties of bacteriophages, including their ability to be engineered for specific targeting and their natural ability to induce immune responses, present significant advantages over conventional treatments.

CONCLUSION

The integration of phage therapy with nanotechnology represents a promising frontier in the fight against breast cancer. This review underscores the need for continued research to address existing challenges and to explore the full potential of phage-based nanomedicines in improving patient outcomes in breast cancer treatment.

Tumor-Targeted Delivery of PD-1-Displaying Bacteriophages by Escherichia coli for Adjuvant Treatment of Colorectal Cancer

Bacteriophages, leveraging phage display and chemical modification, have the potential to deliver large payloads of antitumor agents with precision and to advance vaccine development. However, systemic phage administration often induces neutralizing antibodies, which accelerate phage clearance and reduce accumulation at the target site. To address this limitation, we propose a genetically modified nonpathogenic bacterial strain that specifically targets tumors and releases programmed death ligand 1 (PD-L1)-specific M13 bacteriophage within tumor tissue. We assessed the antitumor efficacy of this phage-expressing strain as an adjunctive therapeutic strategy along with a therapeutic bacterial strain engineered for the controlled release of an immunotoxin. The combination of these strains demonstrated synergistic effects in eliciting antitumor immune responses and inhibiting tumor growth in a murine model of colorectal cancer (CRC). Moreover, when combined with Folfox, the phage-expressing strain significantly extended the survival. This strategy of in vivo expression and tumor-specific release mediated by nonpathogenic bacterial strains provides an effective and safe method for targeted therapeutic phage delivery to tumors.

Preparation of Phage Display cDNA Libraries for Identifying Immunogenic Tumor Antigens: Challenges in Functional cDNA Presentation and Approaches to Overcoming Them

Cancer continues to represent a substantial burden in terms of its morbidity and mortality, underscoring the imperative for the development of novel and efficacious treatment modalities. Recent advances in cancer immunotherapy have highlighted the importance of identifying tumour-specific antigens, which can assist the immune system in targeting malignant cells effectively. Phage display technology has emerged as an effective tool for the discovery of novel antigens through cDNA library screening, representing a significant advancement in the field of immunological research. This review examines the discovery of tumour antigens using phage display technology, emphasising the construction of cDNA libraries, their subsequent display on bacteriophages and the utilisation of diverse biopanning techniques. These elements play a pivotal role in advancing the discovery of novel tumour antigens and the development of targeted cancer therapies. This review addresses the challenges associated with the filamentous phage display of cDNA libraries and proposes strategies to improve the effectiveness of this approach, encouraging further research for clinical applications.

Single-Stranded Variable Fragment Gene Libraries Built for Phage Display: An Updated Review of Design, Selection and Application

The development of the phage display technique has brought practicality and speed when selecting high-affinity molecules. It is used to obtain single-chain variable fragments (scFvs) and has revolutionized several branches of research and industry. These are developed from gene libraries that differ in their construction strategies, which causes a diversity of sequences, specificity and binding strength of the projected molecule to its antigen. In this review, we present the recent studies that demonstrate methods and approaches using immune, naïve, synthetic and semi-synthetic libraries to construct and select scFvs. Subsequently, the characteristics of these libraries, the functionality of the scFvs and the cost-benefits of production will be discussed. In addition, we highlight the methodological trends and challenges to be overcome in order to optimize the production and application of these antibody fragments.

A review of in vitro stochastic and non-stochastic affinity maturation strategies for phage display derived monoclonal antibodies

Monoclonal antibodies identified using display technologies like phage display occasionally suffers from a lack of affinity making it unsuitable for application. This drawback is circumvented with the application of affinity maturation. Affinity maturation is an essential step in the natural evolution of antibodies in the immune system. The evolution of molecular based methods has seen the development of various mutagenesis approaches. This allows for the natural evolutionary process during somatic hypermutation to be replicated in the laboratories for affinity maturation to fine-tune the affinity and selectivity of antibodies. In this review, we will discuss affinity maturation strategies for mAbs generated through phage display systems. The review will highlight various in vitro stochastic and non-stochastic affinity maturation approaches that includes but are not limited to random mutagenesis, site-directed mutagenesis, and gene synthesis.

A new standardization for the use of chicken embryo: selection of target from the phage display library and infection

The filamentous bacteriophage M13KO7 (M13) is the most used in phage display (PD) technology and, like other phages, has been applied in several areas of medicine, agriculture, and in the food industry. One of the advantages is that they can modulate the immune response in the presence of pathogenic microorganisms, such as bacteria and viruses. This study evaluated the use of phage M13 in the chicken embryos model. We inoculated 13-day-old chicken embryos with Salmonella Pullorum (SP) and then evaluated survival for the presence of phage M13 or E. coli ER2738 (ECR) infected with M13. We found that the ECR bacterium inhibits SP multiplication in 0.32 (M13-infected ECR) or 0.44 log UFC/mL (M13-uninfected ECR) and that the ECR-free phage M13 from the PD library can be used in chicken embryo models. This work provides the use of the chicken embryo as a model to study systemic infection and can be employed as an analysis tool for various peptides that M13 can express from PD selection. KEY POINTS: • SP-infected chicken embryo can be a helpful model of systemic infection for different tests. • Phage M13 does not lead to embryonic mortality or cause serious injury to embryos. • Phage M13 from the PD library can be used in chicken embryo model tests.

Phage Display as a Medium for Target Therapy Based Drug Discovery, Review and Update

Phage libraries are now amongst the most prominent approaches for the identification of high-affinity antibodies/peptides from billions of displayed phages in a specific library through the biopanning process. Due to its ability to discover potential therapeutic candidates that bind specifically to targets, phage display has gained considerable attention in targeted therapy. Using this approach, peptides with high-affinity and specificity can be identified for potential therapeutic or diagnostic use. Furthermore, phage libraries can be used to rapidly screen and identify novel antibodies to develop immunotherapeutics. The Food and Drug Administration (FDA) has approved several phage display-derived peptides and antibodies for the treatment of different diseases. In the current review, we provided a comprehensive insight into the role of phage display-derived peptides and antibodies in the treatment of different diseases including cancers, infectious diseases and neurological disorders. We also explored the applications of phage display in targeted drug delivery, gene therapy, and CAR T-cell.

An Engineered M13 Filamentous Nanoparticle as an Antigen Carrier for a Malignant Melanoma Immunotherapeutic Strategy

Bacteriophages, prokaryotic viruses, hold great potential in genetic engineering to open up new avenues for vaccine development. Our study aimed to establish engineered M13 bacteriophages expressing MAGE-A1 tumor peptides as a vaccine for melanoma treatment. Through in vivo experiments, we sought to assess their ability to induce robust immune responses. Using phage display technology, we engineered two M13 bacteriophages expressing MAGE-A1 peptides as fusion proteins with either pVIII or pIIII coat proteins. Mice were intraperitoneally vaccinated three times, two weeks apart, using two different engineered bacteriophages; control groups received a wild-type bacteriophage. Serum samples taken seven days after each vaccination were analyzed by ELISA assay, while splenocytes harvested seven days following the second boost were evaluated by ex vivo cytotoxicity assay. Fusion proteins were confirmed by Western blot and nano-LC-MS/MS. The application of bacteriophages was safe, with no adverse effects on mice. Engineered bacteriophages effectively triggered immune responses, leading to increased levels of anti-MAGE-A1 antibodies in proportion to the administered bacteriophage dosage. Anti-MAGE-A1 antibodies also exhibited a binding capability to B16F10 tumor cells in vitro, as opposed to control samples. Splenocytes demonstrated enhanced CTL cytotoxicity against B16F10 cells. We have demonstrated the immunogenic capabilities of engineered M13 bacteriophages, emphasizing their potential for melanoma immunotherapy.

Propagation, Purification, and Characterization of Bacteriophages for Phage Therapy

Phage therapy is an alternative approach to combat bacterial infections. In this approach, bacteriophages are used as antimicrobial agents due to their properties to infect specific bacterial cells, to propagate inside their hosts, and to lyse host cell to release progeny phages. However, to introduce bacteriophages to clinical or veterinary practice, it is necessary to construct a large library of precisely characterized phages. Therefore, in this chapter, methods for propagation, purification, and microbiological characterization of bacteriophages are presented in the light of their potential use in phage therapy. Isolation of newly discovered bacteriophages from different habitats is also described as it is a preliminary assessment of their efficacy in combating bacterial biofilms and in the treatment of bacterial infections in a simple insect model-Galleria mellonella.

Unraveling the potential of M13 phages in biomedicine: Advancing drug nanodelivery and gene therapy

M13 phages possessing filamentous phage genomes offer the benefits of selective display of molecular moieties and delivery of therapeutic agent payloads with a tolerable safety profile. M13 phage-displayed technology for resembling antigen portions led to the discovery of mimetic epitopes that applied to antibody-based therapy and could be useful in the design of anticancer vaccines. To date, the excremental experiences have engaged the M13 phage in the development of innovative biosensors for detecting biospecies, biomolecules, and human cells with an acceptable limit of detection. Addressing the emergence of antibiotic-resistant bacteria, M13 phages are potent for packaging the programmed gene editing tools, such as CRISPR/Cas, to target multiple antimicrobial genes. Moreover, their display potential in combination with nanoparticles inspires new approaches for engineering targeted theragnostic platforms targeting multiple cellular biomarkers in vivo. In this review, we present the available data on optimizing the use of bacteriophages with a focus on the to date experiences with M13 phages, either as monoagent or as part of combination regimens in the practices of biosensors, vaccines, bactericidal, modeling of specific antigen epitopes, and phage-guided nanoparticles for drug delivery systems. Despite increasing research interest, a deep understanding of the underlying biological and genetic behaviors of M13 phages is needed to enable the full potential of these bioagents in biomedicine, as discussed here. We also discuss some of the challenges that have thus far limited the development and practical marketing of M13 phages.

Generation of a helper phage for the fluorescent detection of peptide-target interactions by dual-display phages

Phage display is a molecular biology technique that allows the presentation of foreign peptides on the surface of bacteriophages. It is widely utilized for applications such as the discovery of biomarkers, the development of therapeutic antibodies, and the investigation of protein-protein interactions. When employing phages in diagnostic and therapeutic monitoring assays, it is essential to couple them with a detection system capable of revealing and quantifying the interaction between the peptide displayed on the phage capsid and the target of interest. This process is often technically challenging and costly. Here, we generated a fluorescent helper phage vector displaying sfGFP in-frame to the pIII of the capsid proteins. Further, we developed an exchangeable dual-display phage system by combining our newly developed fluorescent helper phage vector with a phagemid vector harboring the engineered pVIII with a peptide-probe. By doing so, the sfGFP and a peptide-probe are displayed on the same phage particle. Notably, our dual-display approach is highly flexible as it allows for easy exchange of the displayed peptide-probe on the pVIII to gain the desired selectivity, while maintaining the sfGFP gene, which allows easy visualization and quantification of the interaction peptide-probe. We anticipate that this system will reduce time and costs compared to the current phage-based detection systems.

Exploring shark VNAR antibody against infectious diseases using phage display technology

Antibody with high affinity and specificity to antigen has widely used as a tool to combat various diseases. The variable domain of immunoglobulin new antigen receptor (VNAR) naturally found in shark contains autonomous function as single-domain antibody. Due to its excellent characteristics, the small, non-complex, and highly stable have made shark VNAR can acquires the antigen-binding capability that might not be reached by conventional antibody. Phage display technology enables shark VNAR to be presented on the surface of phage, allowing the exploration of shark VNAR as an alternative antibody format to target antigens from various infectious diseases. The application of phage-displayed shark VNAR in antibody library and biopanning eventually leads to the discovery and isolation of antigen-specific VNARs with diagnostic and therapeutic potential towards infectious diseases. This review provides an overview of the shark VNAR antibody, the types of phage display technology with comparison to the other types of display system, as well as the application and case studies of phage-displayed shark VNAR antibodies against infectious diseases.

Strategies increasing the effectiveness of temozolomide at various levels of anti-GBL therapy

Glioblastoma (GBL) is the most common (60-70% of primary brain tumours) and the most malignant of the glial tumours. Although current therapies remain palliative, they have been proven to prolong overall survival. Within an optimal treatment regimen (incl. surgical resection, radiation therapy, and chemotherapy) temozolomide as the current anti-GBL first-line chemotherapeutic has increased the median overall survival to 14-15 months, and the percentage of patients alive at two years has been reported to rise from 10.4% to 26.5%. Though, the effectiveness of temozolomide chemotherapy is limited by the serious systemic, dose-related side effects. Therefore, the ponderation regarding novel treatment methods along with innovative formulations is crucial to emerging the therapeutic potential of the widely used drug simultaneously reducing the drawbacks of its use. Herein the complex temozolomide application restrictions present at different levels of therapy as well as, the currently proposed strategies aimed at reducing those limitations are demonstrated. Approaches increasing the efficacy of anti-GBL treatment are addressed. Our paper is focused on the most recent developments in the field of nano/biomaterials-based systems for temozolomide delivery and their functionalization towards more effective blood-brain-barrier crossing and/or tumour targeting. Appropriate designing accounting for the physical and chemical features of formulations along with distinct routes of administration is also discussed. In addition, considering the multiple resistance mechanisms, the molecular heterogeneity and the evolution of tumour the purposely selected delivery methods, the combined therapeutic approaches and specifically focused on GBL cells therapies are reviewed.

Generation and characterization of avian single chain variable fragment against human Alpha-Enolase

Overexpression of human alpha-enolase (hEno1)has been reported in a wide range of cancers and is tightly associated with poor prognosis, making it a remarkable biomarker and therapeutic target. In this study, polyclonal yolk-immunoglobulin (IgY) antibodies purified from hEno1-immunized chickens showed a noticeable specific humoral response. Phage display technology was used to construct two antibody libraries of IgY gene-derived single-chain variable fragments (scFvs) containing 7.8 × 10⁷ and 5.4 × 10⁷ transformants, respectively. Phage-based ELISA indicated that specific anti-hEno1 clones were significantly enriched. The nucleotide sequences of scFv-expressing clones were determined and classified into seven groups either in the short linker or the long linker. Moreover, higher mutation rates were revealed in the CDR regions, especially in the CDR3. Three distinguish antigenic epitopes were identified on the hEno1 protein. The binding activities of selected anti-hEno1 scFv on hEno1-positive PE089 lung cancer cells were confirmed using Western blot, flow cytometry, and immunofluorescence assay. In particular, hEnS7 and hEnS8 scFv antibodies significantly suppressed the growth and migration of PE089 cells. Taken together, these chicken-derived anti-hEno1 IgY and scFv antibodies have great potential to develop diagnostic and therapeutic agents for the treatment of lung cancer patients with high expression levels of hEno1 protein.

The variable conversion of neutralizing anti-SARS-CoV-2 single-chain antibodies to IgG provides insight into RBD epitope accessibility

Monoclonal antibody (mAb) therapies have rapidly become a powerful class of therapeutics with applications covering a diverse range of clinical indications. Though most widely used for the treatment of cancer, mAbs are also playing an increasing role in the defense of viral infections, most recently with palivizumab for prevention and treatment of severe RSV infections in neonatal and pediatric populations. In addition, during the COVID-19 pandemic, mAbs provided a bridge to the rollout of vaccines; however, their continued role as a therapeutic option for those at greatest risk of severe disease has become limited due to the emergence of neutralization resistant Omicron variants. Although there are many techniques for the identification of mAbs, including single B cell cloning and immunization of genetically engineered mice, the low cost, rapid throughput and technological simplicity of antibody phage display has led to its widespread adoption in mAb discovery efforts. Here we used our 27-billion-member naïve single-chain antibody (scFv) phage library to identify a panel of neutralizing anti-SARS-CoV-2 scFvs targeting diverse epitopes on the receptor binding domain (RBD). Although typically a routine process, we found that upon conversion to IgG, a number of our most potent clones failed to maintain their neutralization potency. Kinetic measurements confirmed similar affinity to the RBD; however, mechanistic studies provide evidence that the loss of neutralization is a result of structural limitations likely arising from initial choice of panning antigen. Thus this work highlights a risk of scFv-phage panning to mAb conversion and the importance of initial antigen selection.

Identification of a peptide ligand for human ALDH3A1 through peptide phage display: Prediction and characterization of protein interaction sites and inhibition of ALDH3A1 enzymatic activity

Aldehyde dehydrogenase 3A1 (ALDH3A1) by oxidizing medium chain aldehydes to their corresponding carboxylic acids, is involved in the detoxification of toxic byproducts and is considered to play an important role in antioxidant cellular defense. ALDH3A1 has been implicated in various other functions such as cell proliferation, cell cycle regulation, and DNA damage response. Recently, it has been identified as a putative biomarker of prostate, gastric, and lung cancer stem cell phenotype. Although ALDH3A1 has multifaceted functions in both normal and cancer homeostasis, its modes of action are currently unknown. To this end, we utilized a random 12-mer peptide phage display library to identify efficiently human ALDH3A1-interacting peptides. One prevailing peptide (P1) was systematically demonstrated to interact with the protein of interest, which was further validated in vitro by peptide ELISA. Bioinformatic analysis indicated two putative P1 binding sites on the protein surface implying biomedical potential and potent inhibitory activity of the P1 peptide on hALDH3A1 activity was demonstrated by enzymatic studies. Furthermore, in search of potential hALDH3A1 interacting players, a BLASTp search demonstrated that no protein in the database includes the full-length amino acid sequence of P1, but identified a list of proteins containing parts of the P1 sequence, which may prove potential hALDH3A1 interacting partners. Among them, Protein Kinase C Binding Protein 1 and General Transcription Factor II-I are candidates of high interest due to their cellular localization and function. To conclude, this study identifies a novel peptide with potential biomedical applications and further suggests a list of protein candidates be explored as possible hALDH3A1-interacting partners in future studies.

CasPlay provides a gRNA-barcoded CRISPR-based display platform for antibody repertoire profiling

Protein display technologies link proteins to distinct nucleic acid sequences (barcodes), enabling multiplexed protein assays via DNA sequencing. Here, we develop Cas9 display (CasPlay) to interrogate customized peptide libraries fused to catalytically inactive Cas9 (dCas9) by sequencing the guide RNA (gRNA) barcodes associated with each peptide. We first confirm the ability of CasPlay to characterize antibody epitopes by recovering a known binding motif for a monoclonal anti-FLAG antibody. We then use a CasPlay library tiling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome to evaluate vaccine-induced antibody reactivities. Using a peptide library representing the human virome, we demonstrate the ability of CasPlay to identify epitopes across many viruses from microliters of patient serum. Our results suggest that CasPlay is a viable strategy for customized protein interaction studies from highly complex libraries and could provide an alternative to phage display technologies.

Phage Particles of Controlled Length and Genome for In Vivo Targeted Glioblastoma Imaging and Therapeutic Delivery

M13 bacteriophage (phage) are versatile, genetically tunable nanocarriers that have been recently adapted for use as diagnostic and therapeutic platforms. Applying p3 capsid chlorotoxin fusion with the "inho" circular single-stranded DNA (cssDNA) gene packaging system, we produced miniature chlorotoxin inho (CTX-inho) phage particles with a minimum length of 50 nm that can target intracranial orthotopic patient-derived GBM22 glioblastoma tumors in the brains of mice. Systemically administered indocyanine green conjugated CTX-inho phage accumulated in brain tumors, facilitating shortwave infrared detection. Furthermore, we show that our inho phage can carry cssDNA that are transcriptionally active when delivered to GBM22 glioma cells in vitro. The ability to modulate the capsid display, surface loading, phage length, and cssDNA gene content makes the recombinant M13 phage particle an ideal delivery platform.

Neoantigen vaccine and neoantigen-specific cell adoptive transfer therapy in solid tumors: Challenges and future directions

The phenomenon of tumor hierarchy and genetic instability can be explained by the "two-hits theory" and results in the occurrence of many somatic mutations. The expression of nonsynonymous mutations results in the production of mutant proteins from tumor cells, namely tumor-specific antigens called neoantigens. Because neoantigens do not exist in healthy cells, they have the potential to stimulate antitumor immune responses by CD4+ and CD8+ T-cell activation without jeopardizing normal tissues. Immunotherapy has reshaped the cancer treatment paradigm in recent decades with the introduction of immune-checkpoint blockade therapy and transgenic T-cell receptor/chimeric antigen receptor T cells. However, these strategies performed poorly in solid tumors because of the obstacles of the immunosuppressive microenvironment caused by regulatory T cells and other suppressor cells. Therefore, other immunotherapeutic strategies are under development, such as personalized vaccines, to trigger de novo T-cell responses against neoantigens and lead to the amplification of tumor-specific T-cell subclones. Neoantigen epitope prediction algorithms have enabled the detection of neoantigens and the creation of tailored neoantigen vaccines as a result of the fast development of next-generation sequencing and cancer bioinformatics. Here we provide an overview of the current neoantigen cancer vaccines and adoptive T-cell transfer therapy with neoantigen-specific lymphocytes. We also discuss the challenges in developing neoantigen-targeted immunotherapeutic strategies for cancer.

Construction of a T7 phage display nanobody library for bio-panning and identification of chicken dendritic cell-specific binding nanobodies

Dendritic cells (DCs) are the antigen-presenting cells that initiate and direct adaptive immune responses, and thus are critically important in vaccine design. Although DC-targeting vaccines have attracted attention, relevant studies on chicken are rare. A high diversity T7 phage display nanobody library was constructed for bio-panning of intact chicken bone marrow DCs to find DC-specific binding nanobodies. After three rounds of screening, 46 unique sequence phage clones were identified from 125 randomly selected phage clones. Several DC-binding phage clones were selected using the specificity assay. Phage-54, -74, -16 and -121 bound not only with chicken DCs, but also with duck and goose DCs. In vitro, confocal microscopy observation demonstrated that phage-54 and phage-74 efficiently adsorbed onto DCs within 15 min compared to T7-wt. The pull-down assay, however, did not detect any of the previously reported proteins for chicken DCs that could have interacted with the nanobodies displayed on phage-54 and phage-74. Nonetheless, Specified pathogen-free chickens immunized with phage-54 and phage-74 displayed higher levels of anti-p10 antibody than the T7-wt, indicating enhanced antibody production by nanobody mediated-DC targeting. Therefore, this study identified two avian (chicken, duck and goose) DC-specific binding nanobodies, which may be used for the development of DC-targeting vaccines.

Development of a high-throughput method to screen novel antiviral materials

Respiratory infectious diseases pose a serious threat worldwide, and novel antiviral materials are highly demanded. Photocatalytic nanoparticles have been developed to inhibit indirect transmission of pathogens by acting as surface coating materials. During development of such antiviral materials, researchers use bacteriophages as model viruses due to their safety and experimental efficiency. Screening methods are used to identify potential antiviral materials, and better screening technologies will accelerate the discovery of antiviral treatments. In this study, we constructed a novel platform to evaluate antiviral activity of surface coating materials using the M13 bacteriophage and phagemid system derived from phage display technology. The evaluation results generated by this system for the two tested antiviral materials were comparable to those for the materials tested on the Qβ bacteriophage and influenza virus using traditional screening methods. The experimental system developed in this study provides rapid and effective screening and can be applied to the development of novel antiviral materials.

Protein Cages: From Fundamentals to Advanced Applications

Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.

Temperate enterococcal bacteriophages: genetic features and practical application

Temperate bacteriophages are of interest as carriers and vectors of pathogenicity factors that determine an epidemic potential of opportunistic bacteria as well as biotechnology objects. This review describes studies of temperate bacteriophages infecting bacteria of the genus Enterococcus, including strains associated with the development of nosocomial infections. Genetic features of moderate enterococcal phages as well as their potential for practical application in medicine are considered.

Application of phage display for T-cell receptor discovery

The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.

Phage display and other peptide display technologies

Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 "for the phage display of peptides and antibodies". In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine, and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.

Building Personalized Cancer Therapeutics through Multi-Omics Assays and Bacteriophage-Eukaryotic Cell Interactions

Bacteriophage-eukaryotic cell interaction provides the biological foundation of Phage Display technology, which has been widely adopted in studies involving protein-protein and protein-peptide interactions, and it provides a direct link between the proteins and the DNA encoding them. Phage display has also facilitated the development of new therapeutic agents targeting personalized cancer mutations. Proteins encoded by mutant genes in cancers can be processed and presented on the tumor cell surface by human leukocyte antigen (HLA) molecules, and such mutant peptides are called Neoantigens. Neoantigens are naturally existing tumor markers presented on the cell surface. In clinical settings, the T-cell recognition of neoantigens is the foundation of cancer immunotherapeutics. This year, we utilized phage display to successfully develop the 1st antibody-based neoantigen targeting approach for next-generation personalized cancer therapeutics. In this article, we discussed the strategies for identifying neoantigens, followed by using phage display to create personalized cancer therapeutics-a complete pipeline for personalized cancer treatment.

Phage therapy as strategy to face post-antibiotic era: a guide to beginners and experts

Interest in the therapeutic use of bacteriophages (phages) has emerged in recent years, driven mainly by the antimicrobial resistance crisis. This review aimed to summarize some important studies addressing the use of phages as a therapeutic alternative for multiresistant bacterial infections. To this end, a literature search was conducted to address the efficacy and versatility of phage therapy, the advantages and disadvantages of its use, and potential limitations for the application of phage therapy that need to be overcome, especially in Western countries. Thus, this review highlights that phage therapy may be a promising route in the treatment of infections caused by multidrug-resistant pathogens and that a combined approach has the potential to prolong the life of the current available antimicrobials. In addition, standardized clinical trials using monoclonal or polyclonal phages, alone or in combination with antimicrobials, are crucial to determine the real potential of these treatments in clinical practice.

Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs

Next generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material research. However, limitations of traditional phage display hinder the identification process. Growth-based library biases and target-unrelated peptides often result in the dominance of parasitic sequences and the collapse of library diversity. This study describes the effective enrichment of specific peptide motifs potentially binding to arsenic as proof-of-concept using the combination of PSD and NGS. Arsenic is an environmental toxin, which is applied in various semiconductors as gallium arsenide and selective recovery of this element is crucial for recycling and remediation. The development of biomolecules as specific arsenic-binding sorbents is a new approach for its recovery. Usage of NGS for all biopanning fractions allowed for evaluation of motif enrichment, in-depth insight into the selection process and the discrimination of biopanning artefacts, e.g., the amplification-induced library-wide reduction in hydrophobic amino acid proportion. Application of bioinformatics tools led to the identification of an SxHS and a carboxy-terminal QxQ motif, which are potentially involved in the binding of arsenic. To the best of our knowledge, this is the first report of PSD combined with NGS of all relevant biopanning fractions.

Viral Related Tools against SARS-CoV-2

At the end of 2019, a new disease appeared and spread all over the world, the COVID-19, produced by the coronavirus SARS-CoV-2. As a consequence of this worldwide health crisis, the scientific community began to redirect their knowledge and resources to fight against it. Here we summarize the recent research on viruses employed as therapy and diagnostic of COVID-19: (i) viral-vector vaccines both in clinical trials and pre-clinical phases; (ii) the use of bacteriophages to find antibodies specific to this virus and some studies of how to use the bacteriophages themselves as a treatment against viral diseases; and finally, (iii) the use of CRISPR-Cas technology both to obtain a fast precise diagnose of the patient and also the possible use of this technology as a cure.

Resonance assignments of bacteriophage T4 Y04L protein

Phage study draws more attention recently as the bacterial antibiotic resistances become a major threat for global health. Bacteriophage T4 is one of the most studied the phages and the representative of Tevenvirinae subfamily. Since 1950s, T4 phage has been studied more intensively than any other large lytic phages and its biological studies have provided basis for current phage biology as well as other applications. However, among approximately 300 T4 genes, 130 of them still remain uncharacterized. Coded by y04L gene in pin-nrdC intergenic region, Y04L is an example of such proteins whose biological function and mechanism are yet to be addressed. While Pin blocks bacterial Lon protease and thus inhibits bacterial toxin-antitoxin system, NrdC or Glutaredoxin is a specific reducing agent for the phage-induced ribonucleotide reductase. With two interesting neighbouring genes, this 11.9 kDa protein may be functionally related to Pin or NrdC. Here, using solution-state NMR, our near-complete resonance assignment of Y04L provides a basis for future structure determination and further mechanism study.

Selection, preparation and characterization of scFv against human lipocalin 6 by phage display technology

Human lipocalin 6 (hLCN6) is a newly discovered epididymal-specific secreted protein, capable of binding to the head and tail of spermatozoa and involved in sperm maturation. Anti-hLCN6 monoclonal antibody coupled immunomagnetic beads (IMBs) can be effectively used for the separation and forensic identification of sperm cells from mixed stains. But the source of monoclonal antibody is limited. In this study, an immunized mouse phage display antibody library was constructed and the single-chain variable fragments (scFvs) against hLCN6 were screened. The selection was performed using four rounds of biopanning and positive clones were validated by phage ELISA. Two anti-hLCN6 scFv clones with highest affinity were selected and sequencing result showed that the two sequences were identical. After prokaryotic expression and purification, the purified scFv could specifically recognize the hLCN6 in the lysate of human sperm cells and epididymis by western blot analysis, without any cross-reactivity with cellular antigens in female epithelial cells. The dissociation constant (K_d) of anti-hLCN6 scFv was 6.69 × 10^-7 mol/L measured by indirect ELISA. Therefore, our work not only provides a useful tool for further exploration of the biological functions of hLCN6, but also opens up new research avenues for the separation of sperm cells from mixed stains based on immuno-binding reaction.

In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display

mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.

Ribokinase screened from T7 phage displayed Mycobacterium tuberculosis genomic DNA library had good potential for the serodiagnosis of tuberculosis

Tuberculosis caused by Mycobacterium tuberculosis (M. tuberculosis) is the leading cause of death among infectious diseases in the worldwide. Lack of more sensitive and effective diagnostic reagents has increased the awareness of rapid diagnosis for tuberculosis. In this study, T7 phage displayed genomic DNA library of M. tuberculosis was constructed to screen the antigens that specially bind with TB-positive serum from the whole genome of M. tuberculosis and to improve the sensitivity and specificity of tuberculosis serological diagnosis. After three rounds of biopanning, results of DNA sequencing and BLAST analysis showed that 19 positive phages displayed four different proteins and the occurrence frequency of the phage which displayed ribokinase was the highest. The results of indirect ELISA and dot immunoblotting indicated that representative phages could specifically bind to tuberculosis-positive serum. The prokaryotic expression vector containing the DNA sequence of ribokinase gene was then constructed and the recombinant protein was expressed and purified to evaluate the serodiagnosis value of ribokinase. The reactivity of the recombinant ribokinase with different clinical serum was detected and the sensitivities and specificities in tuberculosis serodiagnosis were 90% and 86%, respectively by screening serum from tuberculosis patients (n = 90) and uninfected individuals (n = 90) based on ELISA. Therefore, this study demonstrated that ribokinase had good potential for the serodiagnosis of tuberculosis.

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

BACKGROUND

Leptospirosis is an emerging infectious disease worldwide that can cause high morbidity and mortality rates in humans and animals. The causative spirochetes have reservoirs in mammalian hosts, but there has been limited analysis of the genomes of isolates recovered from animals. The aims of this study were to characterize genomic features of two Leptospira interrogans strains recently isolated from asymptomatic dogs in Thailand (strains CUDO5 and CDUO8), and to perform comparative genome analyses with other strains. Molecular adaptive evolution in L. interrogans as signaled by positive selection also was analyzed.

RESULTS

Whole genome sequence analysis revealed that strains CUDO5 and CUDO8 had genome sizes of approximately 4.9 Mbp with 35.1% GC contents. Using monoclonal antibodies, strains CUDO5 and CUDO8 were identified as serovars Paidjan and Dadas, respectively. These strains harbored genes known to be associated with acute and chronic infections. Using Single Nucleotide Polymorphisms phylogeny (SNPs) with 97 L. interrogans strains, CUDO5 and CUDO8 had closest genetic relatedness with each other. Nevertheless, the serovar determinant region (rfb locus) showed variations in the genes encoding sugar biosynthesis. Amongst 13 representative L. interrogans strains examined for molecular adaptive evolution through positive selection under the site-model of Phylogenetic Analysis of Maximum Likelihood, genes responsible for iron acquisition (tlyA and hbpA), motility (fliN2, flgK, and flhB) and thermal adaptation (lpxD1) were under increased selective pressure.

CONCLUSIONS

L. interrogans serovar Paidjan strain CUDO5 and serovar Dadas strain CUDO8 had close genetic relatedness as analyzed by SNPs phylogeny. They contained genes with established roles in acute and chronic leptospirosis. The rfb locus in both serovars showed gene variation associated with sugar biosynthesis. Positive selection analysis indicated that genes encoding factors involved in motility, temperature adaptation, and iron acquisition were under strong positive selection in L. interrogans. These may be associated with adaptation in the early stages of infection.

Phage antibody library screening for the selection of novel high-affinity human single-chain variable fragment against gastrin receptor: an in silico and in vitro study

BACKGROUND

As a membrane G protein coupled receptors (GPCRs) family, gastrin/cholecystokinin-2 receptor (CCK2R) plays a key role in the initiation and development of gastric cancer.

OBJECTIVES

Targeting CCK2R by immunotherapeutics such as single-chain variable fragments (scFvs) may provide an effective treatment modality against gastric cancer. Thus, the main objective of this study was to isolate scFvs specific to CCK2R.

METHODS

To isolate scFvs specific to the CCK2R, we capitalized on a semi-synthetic diverse phage antibody library (PAL) and a solution-phase biopanning process. The library was panned against a biotinylated peptide of the second extracellular loop (ECL2) of CCK2R. After four rounds of biopanning, the selected soluble scFv clones were screened by enzyme-linked immunosorbent assay (ELISA) and examined for specific binding to the peptide. The selected scFvs were purified using immobilized metal affinity chromatography (IMAC). The binding affinity and specificity of the scFvs were examined by the surface plasmon resonance (SPR), immunoblotting and flow cytometry assays and molecular docking using ZDOCK v3.0.2.

RESULTS

Ten different scFvs were isolated, which displayed binding affinity ranging from 0.68 to 8.0 (nM). Immunoblotting and molecular docking analysis revealed that eight scFvs were able to detect the denatured form of CCK2R protein. Of the isolated scFvs, two scFvs showed high-binding affinity to the human gastric adenocarcinoma AGS cells.

CONCLUSIONS

Based on our findings, a couple of the selected scFvs showed markedly high-binding affinity to immobilized CCK2R peptide and CCK2R-overexpressing AGS cells. Therefore, these scFvs are proposed to serve as targeting and/or treatment agents in the diagnosis and immunotherapy of CCK2R-positive tumors. Graphical abstract ᅟ.

Bordetella bronchiseptica bateriophage suppresses B. bronchiseptica-induced inflammation in swine nasal turbinate cells

The development of therapeutic bacteriophages will provide several benefits based on an understanding the basic physiological dynamics of phage and bacteria interactions for therapeutic use in light of the results of antibiotic abuse. However, studies on bacteriophage therapeutics against microbes are very limited, because of lack of phage stability and an incomplete understanding of the physiological intracellular mechanisms of phage. The major objective of this investigation was to provide opportunity for development of a novel therapeutic treatment to control respiratory diseases in swine. The cytokine array system was used to identify the secreted cytokines/chemokines after Bordetella bronchiseptica infection into swine nasal turbinate cells (PT-K75). We also performed the real-time quantitative PCR method to investigate the gene expression regulated by B. bronchiseptica infection or bacteriophage treatment. We found that B. bronchiseptica infection of PT-K75 induces secretion of many cytokines/chemokines to regulate airway inflammation. Of them, secretion and expression of IL-1β and IL-6 are increased in a dose-dependent manner. Interestingly, membrane-bound mucin production via expression of the Muc1 gene is increased in B. bronchiseptica-infected PT-K75 cells. However, cytokine production and Muc1 gene expression are dramatically inhibited by treatment with a specific B. bronchiseptica bacteriophage (Bor-BRP-1). The regulation of cytokine profiles in B. bronchiseptica-induced inflammation by B. bronchiseptica bacteriophage is essential for avoiding inappropriate inflammatory responses. The ability of bacteriophages to downregulate the immune response by inhibiting bacterial infection emphasizes the possibility of bacteriophage-based therapies as a novel anti-inflammatory therapeutic strategy in swine respiratory tracts.

Controllable Assembly of Flexible Protein Nanotubes for Loading Multifunctional Modules

Viruses with filamentous morphologies, such as tobacco mosaic virus (TMV) and M13 bacteriophage, have long been studied as multivalent nanoscaffolds for loading functional motifs. Structural assembly of the capsid proteins (CPs) of filamentous viruses often requires the presence of DNA or RNA molecules, which has limited their applications. Here, we describe a strategy for controllable assembly of flexible bio-nanotubes consisting of Escherichia coli expressed CP of baculovirus Helicoverpa armigera nucleopolyhedrovirus (HearNPV) in vitro. These protein-only nanotubes were studied as a new structural platform for high-density presentation of multiple active molecules on the exterior surface by direct fusion of the protein of interest to the N-terminus of HearNPV CP (HaCP). Structural characterization using cryoelectron microscopy demonstrated that the HaCP could assemble into two closely related but structurally distinct tube types, suggesting the tunable HaCP interaction network is the major contributor to the flexibility of HaCP nanotubes. Our flexible nanotubes could tolerate larger molecular modifications compared with TMV-based templates and could be used as promising candidates for versatile molecular loading applications.

Bacteriophages: Protagonists of a Post-Antibiotic Era

Despite their long success for more than half a century, antibiotics are currently under the spotlight due to the emergence of multidrug-resistant bacteria. The development of new alternative treatments is of particular interest in the fight against bacterial resistance. Bacteriophages (phages) are natural killers of bacteria and are an excellent tool due to their specificity and ecological safety. Here, we highlight some of their advantages and drawbacks as potential therapeutic agents. Interestingly, phages are not only attractive from a clinical point of view, but other areas, such as agriculture, food control, or industry, are also areas for their potential application. Therefore, we propose phages as a real alternative to current antibiotics.

Construction of genetically engineered M13K07 helper phage for simultaneous phage display of gold binding peptide 1 and nuclear matrix protein 22 ScFv antibody

The most common techniques of antibody phage display are based on the use of M13 filamentous bacteriophages. This study introduces a new genetically engineered M13K07 helper phage displaying multiple copies of a known gold binding peptide on p8 coat proteins. The recombinant helper phages were used to rescue a phagemid vector encoding the p3 coat protein fused to the nuclear matrix protein 22 (NMP22) ScFv antibody. Transmission electron microscopy (TEM), UV-vis absorbance spectroscopy, and field emission scanning electron microscopy (FE-SEM) with energy dispersive X-ray spectroscopy (EDX) analysis revealed that the expression of gold binding peptide 1 (GBP1) on major coat protein p8 significantly enhances the gold-binding affinity of M13 phages. The recombinant bacteriophages at concentrations above 5×10⁴ pfu/ml red-shifted the UV-vis absorbance spectra of gold nanoparticles (AuNPs); however, the surface plasmon resonance of gold nanoparticles was not changed by the wild type bacteriophages at concentrations up to 10¹² pfu/ml. The phage ELISA assay demonstrated the high affinity binding of bifunctional bacteriophages to NMP22 antigen at concentrations of 10⁵ and 10⁶ pfu/ml. Thus, the p3 end of the bifunctional bacteriophages would be able to bind to specific target antigen, while the AuNPs were assembled along the coat of virus for signal generation. Our results indicated that the complex of antigen-bacteriophages lead to UV-vis spectral changes of AuNPs and NMP22 antigen in concentration range of 10-80μg/ml can be detected by bifunctional bacteriophages at concentration of 10⁴ pfu/ml. The ability of bifunctional bacteriophages to bind to antigen and generate signal at the same time, makes this approach applicable for identifying different antigens in immunoassay techniques.

Production and Characterization of Neutralizing Antibodies against Bungarus multicinctus Snake Venom

The venom of the banded krait (Bungarus multicinctus), one of the major venomous species in Taiwan, contains neurotoxic venom proteins (B. multicinctus proteins) that pose a serious medical problem in tropical and subtropical countries. Even though horse-derived serum is an efficient therapy against snake venom, it is associated with a high cost and side effects. Therefore, developing a more cost-effective alternative treatment option is highly envisaged. In this study, chickens were immunized with B. multicinctus proteins, and polyclonal immunoglobulin Y (IgY) antibodies were purified from eggs. IgY showed a binding activity to B. multicinctus proteins that was similar to horse antivenin, and its titer in chickens lasted for at least 6 months. We constructed two antibody libraries by phage display antibody technology, which contain 1.0 × 10⁷ and 2.9 × 10⁸ transformants, respectively. After biopanning, a phage-based enzyme-linked immunosorbent assay (ELISA) indicated that specific clones were enriched. Thirty randomly selected clones expressing monoclonal single-chain variable-fragment (scFv) antibodies were classified into four groups with a short linker and two with a long linker. These selected scFv antibodies showed specific binding activities to B. multicinctus proteins but not to the venomous proteins of other snakes. Most importantly, polyclonal IgY demonstrated a similar neutralization efficiency as did horse-derived antivenin in mice that were injected with a minimum lethal dosage (MLD) of venom proteins. A mixture of several monoclonal anti-B. multicinctus scFv antibodies was also able to partially inhibit the lethal effect on mice. We profoundly believe that IgY and scFv antibodies can be applied in developing diagnostic agents for wound exudates and as an alternative treatment for snakebite envenomation in the future.IMPORTANCE Snake envenomation is one of the global medical issues of concern. Horse-derived antivenin is an effective way to treat snakebites, but it is costly and occasionally causes severe side effects. In this study, we first generated and characterized IgY antibodies with neutralization activity in chickens. Subsequently, we generated a panel of monoclonal scFv antibodies using phage display antibody technology. A mixture of scFv antibodies was able to partially inhibit the lethal effect in mice that were injected with lethal dosages of venom proteins and prolong their survival time. We believe that chicken-derived IgY and scFv antibodies have great potential for the development of diagnostic agents for wound exudates and therapeutic agents against snake envenomation in the future.

Continuous microfluidic assortment of interactive ligands (CMAIL)

Finding an interactive ligand-receptor pair is crucial to many applications, including the development of monoclonal antibodies. Biopanning, a commonly used technique for affinity screening, involves a series of washing steps and is lengthy and tedious. Here we present an approach termed continuous microfluidic assortment of interactive ligands, or CMAIL, for the screening and sorting of antigen-binding single-chain variable antibody fragments (scFv) displayed on bacteriophages (phages). Phages carrying native negative charges on their coat proteins were electrophoresed through a hydrogel matrix functionalized with target antigens under two alternating orthogonal electric fields. During the weak horizontal electric field phase, phages were differentially swept laterally depending on their affinity for the antigen, and all phages were electrophoresed down to be collected during the strong vertical electric field phase. Phages of different affinity were spatially separated, allowing the continuous operation. More than 10⁵ CFU (colony forming unit) antigen-interacting phages were isolated with ~100% specificity from a phage library containing 3 × 10⁹ individual members within 40 minutes of sorting using CMAIL. CMAIL is rapid, sensitive, specific, and does not employ washing, elution or magnetic beads. In conclusion, we have developed an efficient and cost-effective method for isolating and sorting affinity reagents involving phage display.