1
|
Higashi K, Oda S, Fujii M, Nishida F, Matsumoto H, Morise J, Oka S, Nonaka M. Construction of a T7 phage random peptide library by combining seamless cloning with in vitro translation. J Biochem 2023; 175:85-93. [PMID: 37795834 DOI: 10.1093/jb/mvad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/07/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
T7 phage libraries displaying random peptides are powerful tools for screening peptide sequences that bind to various target molecules. The T7 phage system has the advantage of less biased peptide distribution compared to the M13 phage system. However, the construction of T7 phage DNA is challenging due to its long 36 kb linear DNA. Furthermore, the diversity of the libraries depends strongly on the efficiency of commercially available packaging extracts. To address these issues, we examined the combination of seamless cloning with cell-free translation systems. Seamless cloning technologies have been widely used to construct short circular plasmid DNA, and several recent studies showed that cell-free translation can achieve more diverse phage packaging. In this study, we combined these techniques to construct four libraries (CX7C, CX9C, CX11C and CX13C) with different random regions lengths. The libraries thus obtained all showed diversity > 109 plaque forming units (pfu). Evaluating our libraries with an anti-FLAG monoclonal antibody yielded the correct epitope sequence. The results indicate that our libraries are useful for screening peptide epitopes against antibodies. These findings suggest that our system can efficiently construct T7 phage libraries with greater diversity than previous systems.
Collapse
Affiliation(s)
- Katsuaki Higashi
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Sakiho Oda
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Mai Fujii
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Fumiya Nishida
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hayato Matsumoto
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Jyoji Morise
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shogo Oka
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Motohiro Nonaka
- Department of Biological Chemistry, Human Health Sciences, Graduate School of Medicine, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| |
Collapse
|
2
|
Kondo K, Nakano S, Hisatsune J, Sugawara Y, Kataoka M, Kayama S, Sugai M, Kawano M. Characterization of 29 newly isolated bacteriophages as a potential therapeutic agent against IMP-6-producing Klebsiella pneumoniae from clinical specimens. Microbiol Spectr 2023; 11:e0476122. [PMID: 37724861 PMCID: PMC10581060 DOI: 10.1128/spectrum.04761-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/12/2023] [Indexed: 09/21/2023] Open
Abstract
Carbapenemase-producing Enterobacteriaceae (CPE) are one of the most detrimental species of antibiotic-resistant bacteria globally. Phage therapy has emerged as an effective strategy for the treatment of CPE infections. In western Japan, the rise of Klebsiella pneumoniae strains harboring the pKPI-6 plasmid encoding bla IMP-6 is of increasing concern. To address this challenge, we isolated 29 phages from Japanese sewage, specifically targeting 31 K. pneumoniae strains and one Escherichia coli strain harboring the pKPI-6 plasmid. Electron microscopy analysis revealed that among the 29 isolated phages, 21 (72.4%), 5 (17.2%), and 3 (10.3%) phages belonged to myovirus, siphovirus, and podovirus morphotypes, respectively. Host range analysis showed that 18 Slopekvirus strains within the isolated phages infected 25-26 K. pneumoniae strains, indicating that most of the isolated phages have a broad host range. Notably, K. pneumoniae strain Kp21 was exclusively susceptible to phage øKp_21, whereas Kp22 exhibited susceptibility to over 20 phages. Upon administering a phage cocktail composed of 10 phages, we observed delayed emergence of phage-resistant bacteria in Kp21 but not in Kp22. Intriguingly, phage-resistant Kp21 exhibited heightened sensitivity to other bacteriophages, indicating a "trade-off" for resistance to phage øKp_21. Our proposed phage set has an adequate number of phages to combat the K. pneumoniae strain prevalent in Japan, underscoring the potential of a well-designed phage cocktail in mitigating the occurrence of phage-resistant bacteria. IMPORTANCE The emergence of Klebsiella pneumoniae harboring the bla IMP-6 plasmid poses an escalating threat in Japan. In this study, we found 29 newly isolated bacteriophages that infect K. pneumoniae strains carrying the pKPI-6 plasmid from clinical settings in western Japan. Our phages exhibited a broad host range. We applied a phage cocktail treatment composed of 10 phages against two host strains, Kp21 and Kp22, which displayed varying phage susceptibility patterns. Although the phage cocktail delayed the emergence of phage-resistant Kp21, it was unable to hinder the emergence of phage-resistant Kp22. Moreover, the phage-resistant Kp21 became sensitive to other phages that were originally non-infective to the wild-type Kp21 strains. Our study highlights the potential of a well-tailored phage cocktail in reducing the occurrence of phage-resistant bacteria.
Collapse
Affiliation(s)
- Kohei Kondo
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Satoshi Nakano
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Junzo Hisatsune
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Michiyo Kataoka
- Department of Pathology, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Shizuo Kayama
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Mitsuoki Kawano
- Department of Nutritional Sciences, Nakamura Gakuen University, Jonan-Ku, Fukuoka, Japan
| |
Collapse
|
3
|
Aripov VS, Volkova NV, Taranin AV, Mechetina LV, Chikaev NA, Nayakshin AM, Nesmeyanova VS, Isaeva AA, Merkul'eva YA, Shanshin DV, Belenkaya SV, Ilyichev AA, Shcherbakov DN. The Search for Single-Domain Antibodies Interacting with the Receptor-Binding Domain of SARS-CoV-2 Surface Protein. Bull Exp Biol Med 2023:10.1007/s10517-023-05839-6. [PMID: 37464199 DOI: 10.1007/s10517-023-05839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Indexed: 07/20/2023]
Abstract
We performed a search for nanoantibodies that specifically interact with the receptor-binding domain (RBD) of the SARS-CoV-2 surface protein. The specificity of single-domain antibodies from the blood sera of a llama immunized with RBD of SARS-CoV-2 surface protein S (variant B.1.1.7 (Alpha)) was analyzed by ELISA. Recombinant trimers of the SARS-CoV-2 spike protein were used as antigens. In this work, a set of single-domain antibodies was obtained that specifically bind to the RBD of the SARS-CoV-2 virus.
Collapse
Affiliation(s)
- V S Aripov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia.
| | - N V Volkova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A V Taranin
- Institute of Molecular and Cellular Biology, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - L V Mechetina
- Institute of Molecular and Cellular Biology, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Chikaev
- Institute of Molecular and Cellular Biology, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A M Nayakshin
- Institute of Molecular and Cellular Biology, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V S Nesmeyanova
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A A Isaeva
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - Yu A Merkul'eva
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - D V Shanshin
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - S V Belenkaya
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A A Ilyichev
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - D N Shcherbakov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| |
Collapse
|
4
|
Huss P, Chen J, Raman S. High-throughput approaches to understand and engineer bacteriophages. Trends Biochem Sci 2023; 48:187-197. [PMID: 36180320 PMCID: PMC9868059 DOI: 10.1016/j.tibs.2022.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 01/26/2023]
Abstract
Bacteriophage research has been vital to fundamental aspects of modern biology. Advances in metagenomics have revealed treasure troves of new and uncharacterized bacteriophages ('phages') that are not yet understood. However, our ability to find new phages has outpaced our understanding of how sequence encodes function in phages. Traditional approaches for characterizing phages are limited in scale and face hurdles in determining how changes in sequence drive function. We describe powerful emerging technologies that can be used to clarify sequence-function relationships in phages through high-throughput genome engineering. Using these approaches, up to 105 variants can be characterized through pooled selection experiments and deep sequencing. We describe caveats when using these tools and provide examples of basic science and engineering goals that are pursuable using these approaches.
Collapse
Affiliation(s)
- Phil Huss
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jackie Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
5
|
Huang J, Takakusagi Y, Ru B. Editorial: Phage display: Technique and applications. Front Microbiol 2022; 13:1097661. [PMID: 36560941 PMCID: PMC9767457 DOI: 10.3389/fmicb.2022.1097661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China,*Correspondence: Jian Huang
| | - Yoichi Takakusagi
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Beibei Ru
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
6
|
Hayashi T, Yamamoto N, Kurosawa G, Tajima K, Kondo M, Hiramatsu N, Kato Y, Tanaka M, Yamaguchi H, Kurosawa Y, Yamada H, Fujita N. A Novel High-Throughput Screening Method for a Human Multicentric Osteosarcoma-Specific Antibody and Biomarker Using a Phage Display-Derived Monoclonal Antibody. Cancers (Basel) 2022; 14:cancers14235829. [PMID: 36497311 PMCID: PMC9739802 DOI: 10.3390/cancers14235829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Osteosarcoma is a malignant tumor that produces neoplastic bone or osteoid osteoma. In human multicentric osteosarcoma (HMOS), a unique variant of human osteosarcoma (HOS), multiple bone lesions occur simultaneously or asynchronously before lung metastasis. HMOS is associated with an extremely poor prognosis, and effective treatment options are lacking. Using the proteins in our previously generated HMOS cell lines as antigens, we generated antibodies using a human antibody phage library. We obtained antibody clones recognizing 95 independent antigens and developed a fluorescence probe-based enzyme-linked immunosorbent assay (ELISA) technique capable of evaluating the reactivity of these antibodies by fluorescence intensity, allowing simple, rapid, and high-throughput selection of antibody clones. These results were highly correlated with those using flow cytometry. Subsequently, the HMOS cell lysate was incubated with the antibody, the antigen-antibody complex was recovered with magnetic beads, and the protein bands from electrophoresis were analyzed using liquid chromatography-mass spectrometry (LC/MS). CAVIN1/polymerase I transcript release factor was specifically detected in the HMOS cells. In conclusion, we found via a novel high-throughput screening method that CAVIN1/PTRF is an HMOS-specific cell membrane biomarker and an antigen capable of producing human antibodies. In the future, antibody-drug conjugate targeting of these specific proteins may be promising for clinical applications.
Collapse
Affiliation(s)
- Takuma Hayashi
- Department of Orthopedic Surgery, Fujita Health University, Toyoake 470-1192, Japan
| | - Naoki Yamamoto
- Support Office for Bioresource Research, Research Promotion Headquarters, Fujita Health University, Toyoake 470-1192, Japan
- International Center for Cell and Gene Therapy, Research Promotion and Support Headquarters, Fujita Health University, Toyoake 470-1192, Japan
- Correspondence: ; Tel.: +81-562-93-2317
| | - Gene Kurosawa
- International Center for Cell and Gene Therapy, Research Promotion and Support Headquarters, Fujita Health University, Toyoake 470-1192, Japan
| | - Kaori Tajima
- Department of Orthopedic Surgery, Fujita Health University, Toyoake 470-1192, Japan
| | | | - Noriko Hiramatsu
- Support Office for Bioresource Research, Research Promotion Headquarters, Fujita Health University, Toyoake 470-1192, Japan
| | - Yu Kato
- Support Office for Bioresource Research, Research Promotion Headquarters, Fujita Health University, Toyoake 470-1192, Japan
| | - Miho Tanaka
- Center for Joint Research Facilities Support, Research Promotion and Support Headquarters, Fujita Health University, Toyoake 470-1192, Japan
| | - Hisateru Yamaguchi
- Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan
| | - Yoshikazu Kurosawa
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Harumoto Yamada
- Department of Orthopedic Surgery, Fujita Health University, Toyoake 470-1192, Japan
| | - Nobuyuki Fujita
- Department of Orthopedic Surgery, Fujita Health University, Toyoake 470-1192, Japan
| |
Collapse
|
7
|
Abstract
Phage display is a powerful platform for the discovery of novel biologics with high binding affinities to a specific target protein. Here, we describe methods to construct a phage display library containing diverse single-chain variable antibody fragments (scFvs). Specifically, updated methods for polymerase chain reaction (PCR) amplification and fusion of human antibody genes, their ligation into the pComb3X vector for transformation into 5αF'Iq competent bacterial cells, and their expression in M13KO7 helper phage are presented. Additionally, we describe how to amplify and quantify the phage library and to prepare it in various formats for short- and long-term storage. © 2021 Wiley Periodicals LLC. Basic Protocol 1: First-round polymerase chain reaction (PCR) for isolation of antibody fragments Basic Protocol 2: Ethanol precipitation and pooling of fragment DNA Basic Protocol 3: Second-round polymerase chain reaction with splicing by overlap extension (SOE) for antibody fragment fusion Basic Protocol 4: Restriction digestion of individual scFv constructs and pComb3XSS vector Basic Protocol 5: Directional ligation of the scFv constructs and pComb3X backbone Basic Protocol 6: Transformation of pComb-scFv plasmids into 5αF'Iq competent cells Basic Protocol 7: Collection of bacteria containing the scFv library Basic Protocol 8: Preparation of bacterial glycerol stock Basic Protocol 9: Preparation of phage library glycerol stock Basic Protocol 10: Preparation of plasmid DNA stock Basic Protocol 11: Amplification of M13KO7 helper phage Basic Protocol 12: Phage titer by plate assay Alternate Protocol: One-plate phage plaque assay.
Collapse
Affiliation(s)
- Megan A Schladetsch
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut
| | - Andrew J Wiemer
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut
| |
Collapse
|
8
|
Tran P, Kopel J, Fralick JA, Reid TW. The Use of an Organo-Selenium Peptide to Develop New Antimicrobials That Target a Specific Bacteria. Antibiotics (Basel) 2021; 10:611. [PMID: 34063816 DOI: 10.3390/antibiotics10060611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/21/2022] Open
Abstract
This study examines the use of a covalently selenium-bonded peptide and phage that binds to the Yersinia pestis F1 antigen for the targeting and killing of E. coli expressing this surface antigen. Using a Ph.D.-12 phage-display library for affinity selection of the phage which would bind the F1 antigen of Y. pestis, a phage displaying a peptide that binds the F1 antigen with high affinity and specificity was identified. Selenium was then covalently attached to the display phage and the corresponding F1-antigen-binding peptide. Both the phage and peptides with selenium covalently attached retained their binding specificity for the Y. pestis F1 antigen. The phage or peptide not labeled with selenium did not kill the targeted bacteria, while the phage or peptide labeled with selenium did. In addition, the seleno-peptide, expressing the F1 targeting sequence only, killed cells expressing the F1 antigen but not the parent strain that did not express the F1 antigen. Specifically, the seleno-peptide could kill eight logs of bacteria in less than two hours at a 10-µM concentration. These results demonstrate a novel approach for the development of an antibacterial agent that can target a specific bacterial pathogen for destruction through the use of covalently attached selenium and will not affect other bacteria.
Collapse
|
9
|
Abstract
Nosocomial infections (NIs) are hospital-acquired infections which pose a high healthcare burden worldwide. The impact of NIs is further aggravated by the global spread of antimicrobial resistance (AMR). Conventional treatment and disinfection agents are often insufficient to catch up with the increasing AMR and tolerance of the pathogenic bacteria. This has resulted in a need for alternative approaches and raised new interest in therapeutic bacteriophages (phages). In contrast to the limited clinical options available against AMR bacteria, the extreme abundance and biodiversity of phages in nature provides an opportunity to establish an ever-expanding phage library that collectively provides sustained broad-spectrum and poly microbial coverage. Given the specificity of phage-host interactions, phage susceptibility testing can serve as a rapid and cost-effective method for bacterial subtyping. The library can also provide a database for routine monitoring of nosocomial infections as a prelude to preparing ready-to-use phages for patient treatment and environmental sterilization. Despite the remaining obstacles for clinical application of phages, the establishment of phage libraries, pre-stocked phage vials prepared to good manufacturing practice (GMP) standards, and pre-optimized phage screening technology will facilitate efforts to make phages available as modern medicine. This may provide the breakthrough needed to demonstrate the great potential in nosocomial infection management.
Collapse
Affiliation(s)
- Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Tongyu Zhu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
10
|
Duplessis CA, Biswas B. A Review of Topical Phage Therapy for Chronically Infected Wounds and Preparations for a Randomized Adaptive Clinical Trial Evaluating Topical Phage Therapy in Chronically Infected Diabetic Foot Ulcers. Antibiotics (Basel) 2020; 9:antibiotics9070377. [PMID: 32635429 PMCID: PMC7400337 DOI: 10.3390/antibiotics9070377] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 11/21/2022] Open
Abstract
The advent and increasing prevalence of antimicrobial resistance commensurate with the absence of novel antibiotics on the horizon raises the specter of untreatable infections. Phages have been safely administered to thousands of patients exhibiting signals of efficacy in many experiencing infections refractory to antecedent antibiotics. Topical phage therapy may represent a convenient and efficacious treatment modality for chronic refractory infected cutaneous wounds spanning all classifications including venous stasis, burn-mediated, and diabetic ulcers. We will initially provide results from a systematic literature review of topical phage therapy used clinically in refractorily infected chronic wounds. We will then segue into a synopsis of the preparations for a forthcoming phase II a randomized placebo-controlled clinical trial assessing the therapeutic efficacy exploiting adjunctive personalized phage administration, delivered topically, intravenously (IV) and via a combination of both modalities (IV + topical) in the treatment of infected diabetic foot ulcers (perhaps the canonical paradigm representing complicated recalcitrant infected cutaneous wounds).
Collapse
|
11
|
Zhang XQ, Yu LT, Du P, Yin TQ, Zhang ZY, Xu Y, Li X, Li YJ, Wang M, Luo C. Single-chain Antibody Against Reg4 Suppresses Gastric Cancer Cell Growth and Enhances 5-FU-induced Cell Death in vitro. Anticancer Agents Med Chem 2020; 19:610-619. [PMID: 30465515 DOI: 10.2174/1871520619666181122104720] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/15/2018] [Accepted: 11/13/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Regenerating islet-derived gene family member 4 (Reg4), a well-investigated growth factor in the regenerative pancreas, has recently been reported to be highly associated with a majority of gastrointestinal cancers. Pathological hyper-expression or artificial over-expression of Reg4 causes acceleration of tumor growth, migration, and resistance to chemotherapeutic 5-Fluorouracil (5-FU). Until now, no method has been successfully established for eliminating the effects of Reg4 protein. METHODS This study reports the production of an engineered immunoglobin, a single-chain variable fragment (scFv-Reg4), to specifically bind Reg4 and block the bioactivity. The complementary-determining regions (CDRs) against Reg4 were assigned using MOE and ZDOCK servers. The binding affinity (KD) was determined by bio-layer interferometry (BLI). MKN45 and AGS cell proliferation was determined by Thiazolyl blue tetrazolium bromide (MTT) method and the cell apoptosis was detected by flow cytometry assay. RESULTS The KD of scFv-Reg4 to Reg4 was determined to be 1.91×10-8. In MKN45 and AGS cell lines, scFv- Reg4 depressed Reg4-stimulated cell proliferation and the inhibitory rates were 27.7±1.5% and 17.3±2.6%, respectively. Furthermore, scFv significantly enhanced 5-FU-induced cell death, from 23.0±1.0% to 28.4±1.2% in MKN45 and 28.2±0.7% to 36.6±0.6% in AGS cells. Treatment with scFv alone could lyse cancer cells to a certain extent, but no significance has been observed. CONCLUSION The single-chain antibody (scFv-Reg4) significantly inhibited gastric cancer cell proliferation and synergistically enhanced the lethal effect of 5-FU. Thus, traditional chemo-/radio- therapeutics supplemented with scFv-Reg4 may provide advances in the strategy for gastrointestinal cancer treatment.
Collapse
Affiliation(s)
- Xue-Qing Zhang
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Lu-Ting Yu
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China.,Fraser Laboratories for Diabetes Research, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Pei Du
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Tian-Qi Yin
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Zhi-Yuan Zhang
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Ying Xu
- Jiangsu Celtec Biotechnology Co. Ltd, Jiangsu, China
| | - Xiang Li
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - You-Jie Li
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Min Wang
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Nature Medicines, China Pharmaceutical University, Nanjing, China
| | - Chen Luo
- School of Life Science & Technology, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Nature Medicines, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
12
|
Yakushiji H, Kobayashi K, Takenaka F, Kishi Y, Shinohara M, Akehi M, Sasaki T, Ohno E, Matsuura E. Novel single-chain variant of antibody against mesothelin established by phage library. Cancer Sci 2019; 110:2722-2733. [PMID: 31461572 PMCID: PMC6726835 DOI: 10.1111/cas.14150] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/18/2019] [Accepted: 07/21/2019] [Indexed: 01/29/2023] Open
Abstract
Mesothelin (MSLN) shows increased expression in various cancer cells. For clinical application of antibodies as a positron emission tomography (PET) imaging reagent, a human shortened antibody is essential both for avoiding redundant immune responses and for providing rapid imaging. Therefore, we cloned a single‐chain fragment of variable regions (scFv) from a human‐derived gene sequence. This was achieved through the construction of a naïve phage library derived from human tonsil lymphocytes. Using a column with human recombinant MSLN, we carried out bio‐panning of phage‐variants by colony formation. We first obtained 120 clones that were subjected to selection in an ELISA using human recombinant MSLN as a solid phase antigen, and 15 phage clones of scFv with a different sequence were selected and investigated by flow cytometry (FCM). Then, six variants were selected and the individual scFv gene was synthesized in the VL and VH domains and expressed in Chinese hamster ovary cells. Mammalian cell‐derived human‐origin scFv clones were analyzed by FCM again, and one MSLN highly specific scFv clone was established. PET imaging by 89Zr‐labeled scFv was done in mice bearing xenografts with MSLN‐expressing cancer cells, and tumor legions were successfully visualized. The scFv variant established in the present study may be potentially useful for cancer diagnosis by PET imaging.
Collapse
Affiliation(s)
- Hiromasa Yakushiji
- Department of Cell Chemistry, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan.,Department of Medical Life Science Faculty of Medical Bioscience Kyushu, University of Health and Welfare, Miyazaki, Japan
| | - Kazuko Kobayashi
- Department of Cell Chemistry, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan.,Collaborative Research Center for OMIC, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Fumiaki Takenaka
- Collaborative Research Center for OMIC, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Yoshiro Kishi
- Department of Research and Development, Ina Institute, Medical & Biological Laboratories, Co., Ltd, Ina, Japan
| | - Midori Shinohara
- Department of Research and Development, Ina Institute, Medical & Biological Laboratories, Co., Ltd, Ina, Japan
| | - Masaru Akehi
- Collaborative Research Center for OMIC, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Takanori Sasaki
- Collaborative Research Center for OMIC, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Eiji Ohno
- Department of Medical Technology and Sciences, Faculty of Health Sciences, Kyoto Tachibana University, Kyoto, Japan
| | - Eiji Matsuura
- Department of Cell Chemistry, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan.,Collaborative Research Center for OMIC, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan.,Neutron Therapy Research Center, Okayama University, Okayama, Japan
| |
Collapse
|
13
|
Abstract
To support antibody therapeutic development, the crystal structures of a set of 16 germline variants composed of 4 different kappa light chains paired with 4 different heavy chains have been determined. All four heavy chains of the antigen-binding fragments (Fabs) have the same complementarity-determining region (CDR) H3 that was reported in an earlier Fab structure. The structure analyses include comparisons of the overall structures, canonical structures of the CDRs and the VH:VL packing interactions. The CDR conformations for the most part are tightly clustered, especially for the ones with shorter lengths. The longer CDRs with tandem glycines or serines have more conformational diversity than the others. CDR H3, despite having the same amino acid sequence, exhibits the largest conformational diversity. About half of the structures have CDR H3 conformations similar to that of the parent; the others diverge significantly. One conclusion is that the CDR H3 conformations are influenced by both their amino acid sequence and their structural environment determined by the heavy and light chain pairing. The stem regions of 14 of the variant pairs are in the ‘kinked’ conformation, and only 2 are in the extended conformation. The packing of the VH and VL domains is consistent with our knowledge of antibody structure, and the tilt angles between these domains cover a range of 11 degrees. Two of 16 structures showed particularly large variations in the tilt angles when compared with the other pairings. The structures and their analyses provide a rich foundation for future antibody modeling and engineering efforts.
Collapse
Affiliation(s)
| | - Galina Obmolova
- a Janssen Research & Development LLC, Spring House , PA , USA
| | - Thomas J Malia
- a Janssen Research & Development LLC, Spring House , PA , USA
| | - Jinquan Luo
- a Janssen Research & Development LLC, Spring House , PA , USA
| | - Salman Muzammil
- a Janssen Research & Development LLC, Spring House , PA , USA
| | - Raymond Sweet
- a Janssen Research & Development LLC, Spring House , PA , USA
| | | | | |
Collapse
|
14
|
Wang X, Kim HY, Wahlberg B, Edwards WB. Selection and characterization of high affinity VEGFR1 antibodies from a novel human binary code scFv phage library. Biochem Biophys Rep 2015; 3:169-174. [PMID: 26457328 PMCID: PMC4594834 DOI: 10.1016/j.bbrep.2015.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
VEGFR1 is a receptor tyrosine kinase that has been implicated in cancer pathogenesis. It is upregulated in angiogenic endothelial cells and expressed on human tumor cells as well. VEGFR1 positive hematopoietic progenitor cells home to sites of distant metastases prior to the arrival of the tumor cells thus establishing a pre-metastatic niche. To discover high affinity human antibodies selective for VEGFR1 molecular imaging or for molecularly targeted therapy, a novel phage display scFv library was assembled and characterized. The library was constructed from the humanized 4D5 framework that was mostly comprised tyrosine and serine residues in four complimentarity determining regions (CDRs). The library produced diverse and functional antibodies against a panel of proteins, some of which are of biomedical interest including, CD44, VEGFA, and VEGFR1. After panning, these antibodies had affinity strong enough for molecular imaging or targeted drug delivery without the need for affinity maturation. One of the anti-VEGFR1 scFvs recognized its cognate receptor and was selective for the VEGFR1. VEGFR1 contributes to the pathogenesis cancer. To obtain VEGFR1 specific antibodies, a phage displayed scFv library was constructed. Four complimentarity determining regions were principally comprised of tyrosine and serine. High affinity antibody fragments were isolated and characterized. This is the first human antibody fragment specific for VEGFR1 from a phage displayed library.
Collapse
Affiliation(s)
- Xiaolei Wang
- Molecular Imaging Laboratory, Department of Radiology, University of Pittsburgh, Pittsburgh, PA 15219
| | - Hye-Yeong Kim
- Cardiovascular Molecular Imaging Laboratory, Section of Cardiovascular Medicine and Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, 06520
| | - Brendon Wahlberg
- Molecular Imaging Laboratory, Department of Radiology, University of Pittsburgh, Pittsburgh, PA 15219
| | - W Barry Edwards
- Molecular Imaging Laboratory, Department of Radiology, University of Pittsburgh, Pittsburgh, PA 15219
| |
Collapse
|
15
|
Sánchez-Martín D, Martínez-Torrecuadrada J, Teesalu T, Sugahara KN, Alvarez-Cienfuegos A, Ximénez-Embún P, Fernández-Periáñez R, Martín MT, Molina-Privado I, Ruppen-Cañás I, Blanco-Toribio A, Cañamero M, Cuesta AM, Compte M, Kremer L, Bellas C, Alonso-Camino V, Guijarro-Muñoz I, Sanz L, Ruoslahti E, Alvarez-Vallina L. Proteasome activator complex PA28 identified as an accessible target in prostate cancer by in vivo selection of human antibodies. Proc Natl Acad Sci U S A 2013; 110:13791-6. [PMID: 23918357 DOI: 10.1073/pnas.1300013110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Antibody cancer therapies rely on systemically accessible targets and suitable antibodies that exert a functional activity or deliver a payload to the tumor site. Here, we present proof-of-principle of in vivo selection of human antibodies in tumor-bearing mice that identified a tumor-specific antibody able to deliver a payload and unveils the target antigen. By using an ex vivo enrichment process against freshly disaggregated tumors to purge the repertoire, in combination with in vivo biopanning at optimized phage circulation time, we have identified a human domain antibody capable of mediating selective localization of phage to human prostate cancer xenografts. Affinity chromatography followed by mass spectrometry analysis showed that the antibody recognizes the proteasome activator complex PA28. The specificity of soluble antibody was confirmed by demonstrating its binding to the active human PA28αβ complex. Whereas systemically administered control phage was confined in the lumen of blood vessels of both normal tissues and tumors, the selected phage spread from tumor vessels into the perivascular tumor parenchyma. In these areas, the selected phage partially colocalized with PA28 complex. Furthermore, we found that the expression of the α subunit of PA28 [proteasome activator complex subunit 1 (PSME1)] is elevated in primary and metastatic human prostate cancer and used anti-PSME1 antibodies to show that PSME1 is an accessible marker in mouse xenograft tumors. These results support the use of PA28 as a tumor marker and a potential target for therapeutic intervention in prostate cancer.
Collapse
|
16
|
Fagbohun OA, Bedi D, Grabchenko NI, Deinnocentes PA, Bird RC, Petrenko VA. Landscape phages and their fusion proteins targeted to breast cancer cells. Protein Eng Des Sel 2012; 25:271-83. [PMID: 22490956 PMCID: PMC3357133 DOI: 10.1093/protein/gzs013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/19/2012] [Accepted: 02/27/2012] [Indexed: 01/19/2023] Open
Abstract
Breast cancer is a leading cause of death among women in the USA. The efficacy of existing anticancer therapeutics can be improved by targeting them through conjugation with ligands binding to cellular receptors. Recently, we developed a novel drug targeting strategy based on the use of pre-selected cancer-specific 'fusion pVIII proteins' (fpVIII), as targeting ligands. To study the efficiency of this approach in animal models, we developed a panel of breast cancer cell-binding phages as a source of targeted fpVIIIs. Two landscape phage peptide libraries (8-mer f8/8 and 9-mer f8/9) were screened to isolate 132 phage variants that recognize breast carcinoma cells MCF-7 and ZR-75-1 and internalize into the cells. When tested for their interaction with the breast cancer cells in comparison with liver cancer cells HepG2, human mammary cells MCF-10A cells and serum, 16 of the phage probes selectively interacted with the breast cancer cells whereas 32 bound both breast and liver cancer cells. The most prominent cancer-specific phage DMPGTVLP, demonstrating sub-nanomolar Kd in interaction with target cells, was used for affinity chromatography of cellular membrane molecules to reveal its potential binding receptor. The isolated protein was identified by direct sequencing as cellular surface nucleolin. This conclusion was confirmed by inhibition of the phage-cell interaction with nucleolin antibodies. Other prominent phage binders VPTDTDYS, VEEGGYIAA, and DWRGDSMDS demonstrate consensus motifs common to previously identified cancer-specific peptides. Isolated phage proteins exhibit inherent binding specificity towards cancer cells, demonstrating the functional activity of the selected fused peptides. The selected phages, their peptide inserts and intact fusion proteins can serve as promising ligands for the development of targeted nanomedicines and their study in model mice with xenograft of human cells MCF-7 and ZR-75-1.
Collapse
Affiliation(s)
| | | | | | | | | | - Valery A. Petrenko
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
17
|
Kuzmicheva G, Jayanna P, Sorokulova I, Petrenko V. Diversity and censoring of landscape phage libraries. Protein Eng Des Sel 2009; 22:9-18. [PMID: 18988692 PMCID: PMC2640155 DOI: 10.1093/protein/gzn060] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 09/30/2008] [Accepted: 10/07/2008] [Indexed: 11/12/2022] Open
Abstract
Libraries of random peptides displayed on the surface of filamentous phages are a valuable source for biospecific ligands. However, their successful use can be hindered by a disproportionate representation of different phage clones and fluctuation of their composition that arises during phage reproduction, which have potential to affect efficiency of selection of clones with an optimal binding. Therefore, there is a need to develop phage display libraries with extended and varied repertoires of displayed peptides. In this work, we compared the complexity, evolution and representation of two phage display libraries displaying foreign octamers and nonamers in 4000 copies as the N-terminal part of the major coat protein pVIII of phage fd-tet (landscape libraries). They were obtained by replacement of amino acids 2-4 and 2-5 of pVIII with random octa- and nonamers, respectively. Statistical analysis of the libraries revealed their dramatic censoring and evolution during amplification. Further, a survey of both libraries for clones that bind common selectors revealed the presence of different non-overlapping families of target-specific clones in each library justifying the concept that different landscape libraries cover different areas of a sequence space.
Collapse
Affiliation(s)
| | | | | | - V.A. Petrenko
- Department of Pathobiology, Auburn University, t252 Greene Hall, College of Veterinary Medicine, Auburn, AL 36849, USA
| |
Collapse
|
18
|
Abstract
Filamentous phages are thread-shaped bacterial viruses. Their outer coat is a tube formed by thousands equal copies of the major coat protein pVIII. Libraries of random peptides fused to pVIII domains were used for selection of phages probes specific for a panel of test antigens and biological threat agents. Because the viral carrier in the phage borne bio-selective probes is infective, they can be cloned individually and propagated indefinitely without needs of their chemical synthesis or reconstructing. As a new bioselective material, landscape phages combine unique characteristics of affinity reagents and self assembling proteins. Biorecognition layers formed by the phage-derived probes bind biological agents with high affinity and specificity and generate detectable signals in analytical platforms. The performance of phage-derived materials as biorecognition interface was illustrated by detection of Bacillus anthracis spores and Salmonella typhimurium cells. With further refinement, the phage-derived analytical platforms for detecting and monitoring of numerous threat agents may be developed, since phage interface against any bacteria, virus or toxin may be readily selected from the landscape phage libraries. As an interface in the field-use detectors, they may be superior to antibodies, since they are inexpensive, highly specific and strong binders, resistant to high temperatures and environmental stresses.
Collapse
|
19
|
Kouskoff V, Famiglietti S, Lacaud G, Lang P, Rider JE, Kay BK, Cambier JC, Nemazee D. Antigens varying in affinity for the B cell receptor induce differential B lymphocyte responses. J Exp Med 1998; 188:1453-64. [PMID: 9782122 PMCID: PMC2213405 DOI: 10.1084/jem.188.8.1453] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/1998] [Revised: 08/04/1998] [Indexed: 11/04/2022] Open
Abstract
The B cell receptor (BCR) triggers a variety of biological responses that differ depending upon the properties of the antigen. A panel of M13 phage-displayed peptide ligands with varying affinity for the 3-83 antibody was generated to explore the role of antigen-BCR affinity in cell activation studies using primary 3-83 transgenic mouse B cells. Multiple parameters of activation were measured. T cell-independent B cell proliferation, antibody secretion, induction of germline immunoglobulin gamma1 transcripts, and B cell production of interleukin (IL) 2 and interferon gamma responses were better correlated with antigen-BCR affinity than with receptor occupancy. In contrast, other responses, such as upregulation of major histocompatibility complex class II and B7.2 (CD86), secretion of IL-6, and B cell proliferation in the context of CD40 signaling were only weakly dependent on antigen affinity. Biochemical analysis revealed that at saturating ligand concentrations the ability of phage to stimulate some early signaling responses, such as Ca++ mobilization and tyrosine phosphorylation of syk or Igalpha, was highly affinity dependent, whereas the ability to stimulate Lyn phosphorylation was less so. These data suggest that the BCR is capable of differential signaling. The possibility that differential BCR signaling by antigen determines whether an antibody response will be T independent or dependent is discussed.
Collapse
Affiliation(s)
- V Kouskoff
- Department of Pediatrics, National Jewish Medical and Research Center, Denver, Colorado 80206, USA
| | | | | | | | | | | | | | | |
Collapse
|