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Kaneko N, Kurata M, Yamamoto T, Sakamoto A, Takada Y, Kosako H, Takeda H, Sawasaki T, Masumoto J. CANE, a Component of the NLRP3 Inflammasome, Promotes Inflammasome Activation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:86-95. [PMID: 38787200 DOI: 10.4049/jimmunol.2300175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
The nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3 (NLRP3, also called cryopyrin) inflammasome is an intracellular innate immune complex, which consists of the pattern-recognition receptor NLRP3, the adaptor apoptosis-assciated speck-like protein containing a caspase recruitment domain, and procaspase-1. Aberrant activation of the NLRP3 inflammasome causes an autoinflammatory disease called cryopyrin-associated periodic syndrome (CAPS). CAPS is caused by gain-of-function mutations in the NLRP3-encoding gene CIAS1; however, the mechanism of CAPS pathogenesis has not been fully understood. Thus, unknown regulators of the NLRP3 inflammasome, which are associated with CAPS development, are being investigated. To identify novel components of the NLRP3 inflammasome, we performed a high-throughput screen using a human protein array, with NLRP3 as the bait. We identified a NLRP3-binding protein, which we called the cryopyrin-associated nano enhancer (CANE). We demonstrated that CANE increased IL-1β secretion after NLRP3 inflammasome reconstitution in human embryonic kidney 293T cells and formed a "speck" in the cytosol, a hallmark of NLRP3 inflammasome activity. Reduced expression of endogenous CANE decreased IL-1β secretion upon stimulation with the NLRP3 agonist nigericin. To investigate the role of CANE in vivo, we developed CANE-transgenic mice. The PBMCs and bone marrow-derived macrophages of CANE-transgenic mice exhibited increased IL-1β secretion. Moreover, increased autoinflammatory neutrophil infiltration was observed in the s.c. tissue of CANE-transgenic versus wild-type mice; these phenotypes were consistent with those of CAPS model mice. These findings suggest that CANE, a component of the NLRP3 inflammasome, is a potential modulator of the inflammasome and a contributor to CAPS pathogenesis.
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Affiliation(s)
- Naoe Kaneko
- Department of Pathology, Proteo-Science Center and Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Mie Kurata
- Department of Pathology, Proteo-Science Center and Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Toshihiro Yamamoto
- Department of Pathology, Proteo-Science Center and Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Akimasa Sakamoto
- Department of Pathology, Proteo-Science Center and Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
- Department of Hepatobiliary Pancreatic and Transplantation Surgery, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Yasutsugu Takada
- Department of Hepatobiliary Pancreatic and Transplantation Surgery, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Hiroyuki Takeda
- Division of Proteo-Drug-Discovery Sciences, Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
| | - Junya Masumoto
- Department of Pathology, Proteo-Science Center and Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
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Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy S. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. Nucleic Acids Res 2024; 52:e47. [PMID: 38709890 PMCID: PMC11162764 DOI: 10.1093/nar/gkae332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.
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Affiliation(s)
- Weiyi Li
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Xianan Liu
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Han Mei
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Po-Hsiang Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
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Matsuda KM, Sugimoto E, Ako Y, Kitamura M, Miyahara M, Kotani H, Norimatsu Y, Hisamoto T, Kuzumi A, Fukasawa T, Sato S, Yoshizaki A. Reliability, validity, and sensitivity of the Japanese version of the University of California Los Angeles scleroderma clinical trial consortium gastrointestinal tract instrument: Application to efficacy assessment of intravenous immunoglobulin administration. J Dermatol 2024; 51:741-751. [PMID: 38558171 DOI: 10.1111/1346-8138.17202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/23/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
This study aimed to develop and assess the reliability, validity, and sensitivity of the Japanese version of the University of California Los Angeles Scleroderma Clinical Trial Consortium gastrointestinal tract (GIT) Instrument 2.0 (the GIT score), as an evaluation tool for GIT symptoms in systemic sclerosis (SSc). The Japanese version of the GIT score was constructed using the forward-backward method. The reliability and validity of this instrument were evaluated in a cohort of 38 SSc patients. Correlation analysis was conducted to assess the relationship between the GIT score and existing patient-reported outcome measures. Additionally, the sensitivity of the GIT score was examined by comparing GIT scores before and after intravenous immunoglobulin (IVIG) administration in 10 SSc-myositis overlap patients, as IVIG has recently demonstrated effectiveness in alleviating GIT symptoms of SSc. As a result, the Japanese version of the GIT score exhibited internal consistency and a significant association with the Frequency Scale for the Symptoms of Gastroesophageal Reflux Disease. Furthermore, the total GIT score, as well as the reflux and distention/bloating subscales, displayed moderate correlations with the EuroQol 5 dimensions (EQ-5D) pain/discomfort subscale and the Short Form-36 body pain subscale. Notably, following IVIG treatment, there was a statistically significant reduction in the total GIT score and multiple subscales. We first validated the Japanese version of the GIT score in Japanese SSc patients in real-world clinical settings. This instrument holds promise for application in future clinical trials involving this patient population.
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Affiliation(s)
- Kazuki M Matsuda
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eiki Sugimoto
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiaki Ako
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Marie Kitamura
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mai Miyahara
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirohito Kotani
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuta Norimatsu
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Teruyoshi Hisamoto
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ai Kuzumi
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takemichi Fukasawa
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Clinical Cannabinoid Research, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinichi Sato
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ayumi Yoshizaki
- Department of Dermatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Clinical Cannabinoid Research, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Takeda H. Autoantibody Profiling Using Human Autoantigen Protein Array and AlphaScreen. Methods Mol Biol 2024; 2766:107-128. [PMID: 38270871 DOI: 10.1007/978-1-0716-3682-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Autoantibodies that recognize self-antigens are believed to have a close relationship with diseases such as autoimmune diseases, cancer, and lifestyle diseases. Analysis of autoantibodies is essential for investigating pathology mechanisms, diagnosis, and therapeutics of these diseases. We developed an autoantibody profiling assay using a cell-free synthesized protein array and high-throughput screening technology. Our assay system can sensitively detect interaction between recombinant antigen protein and autoantibody and efficiently analyze autoantibody profiling in patients' sera.
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Affiliation(s)
- Hiroyuki Takeda
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan.
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Maharjan A, Park JH. Cell-free protein synthesis system: A new frontier for sustainable biotechnology-based products. Biotechnol Appl Biochem 2023; 70:2136-2149. [PMID: 37735977 DOI: 10.1002/bab.2514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Cell-free protein synthesis (CFPS) system is an innovative technology with a wide range of potential applications that could challenge current thinking and provide solutions to environmental and health issues. CFPS system has been demonstrated to be a successful way of producing biomolecules in a variety of applications, including the biomedical industry. Although there are still obstacles to overcome, its ease of use, versatility, and capacity for integration with other technologies open the door for it to continue serving as a vital instrument in synthetic biology research and industry. In this review, we mainly focus on the cell-free based platform for various product productions. Moreover, the challenges in the bio-therapeutic aspect using cell-free systems and their future prospective for the improvement and sustainability of the cell free systems.
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Affiliation(s)
- Anoth Maharjan
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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6
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Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy SF. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562064. [PMID: 37873145 PMCID: PMC10592806 DOI: 10.1101/2023.10.13.562064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45,000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.
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Affiliation(s)
- Weiyi Li
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Xianan Liu
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Han Mei
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Po-Hsiang Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
- Present Address: BacStitch DNA, Los Altos, CA, USA
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7
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Kuzumi A, Norimatsu Y, Matsuda KM, Ono C, Okumura T, Kogo E, Goshima N, Fukasawa T, Fushida N, Horii M, Yamashita T, Yoshizaki-Ogawa A, Yamaguchi K, Matsushita T, Sato S, Yoshizaki A. Comprehensive autoantibody profiling in systemic autoimmunity by a highly-sensitive multiplex protein array. Front Immunol 2023; 14:1255540. [PMID: 37701440 PMCID: PMC10493387 DOI: 10.3389/fimmu.2023.1255540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023] Open
Abstract
Comprehensive autoantibody evaluation is essential for the management of autoimmune disorders. However, conventional methods suffer from poor sensitivity, low throughput, or limited availability. Here, using a proteome-wide human cDNA library, we developed a novel multiplex protein assay (autoantibody array assay; A-Cube) covering 65 antigens of 43 autoantibodies that are associated with systemic sclerosis (SSc) and polymyositis/dermatomyositis (PM/DM). The performance of A-Cube was validated against immunoprecipitation and established enzyme-linked immunosorbent assay. Further, through an evaluation of serum samples from 357 SSc and 172 PM/DM patients, A-Cube meticulously illustrated a diverse autoantibody landscape in these diseases. The wide coverage and high sensitivity of A-Cube also allowed the overlap and correlation analysis between multiple autoantibodies. Lastly, reviewing the cases with distinct autoantibody profiles by A-Cube underscored the importance of thorough autoantibody detection. Together, these data highlighted the utility of A-Cube as well as the clinical relevance of autoantibody profiles in SSc and PM/DM.
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Affiliation(s)
- Ai Kuzumi
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yuta Norimatsu
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kazuki M. Matsuda
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | | | | | - Emi Kogo
- ProteoBridge Corporation, Tokyo, Japan
| | - Naoki Goshima
- ProteoBridge Corporation, Tokyo, Japan
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takemichi Fukasawa
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Clinical Cannabinoid Research, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Natsumi Fushida
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Motoki Horii
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Takashi Yamashita
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Asako Yoshizaki-Ogawa
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kei Yamaguchi
- ProteoBridge Corporation, Tokyo, Japan
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takashi Matsushita
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Shinichi Sato
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Ayumi Yoshizaki
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Clinical Cannabinoid Research, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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Matsuda KM, Kotani H, Yamaguchi K, Okumura T, Fukuda E, Kono M, Hisamoto T, Kawanabe R, Norimatsu Y, Kuzumi A, Fukayama M, Fukasawa T, Ebata S, Yoshizaki-Ogawa A, Okamura T, Shoda H, Fujio K, Goshima N, Sato S, Yoshizaki A. Significance of anti-transcobalamin receptor antibodies in cutaneous arteritis revealed by proteome-wide autoantibody screening. J Autoimmun 2023; 135:102995. [PMID: 36724643 DOI: 10.1016/j.jaut.2023.102995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 02/03/2023]
Abstract
Cutaneous arteritis (CA) is a single-organ vasculitis that exclusively affects the small to medium-sized arteries of the skin. Diagnosis depends on a histological investigation with skin biopsy, which could be burdensome for both patients and clinicians. Moreover, the pathogenesis of CA remains unstudied, and treatment has not yet been established. Herein, we applied our proteome-wide autoantibody screening method to explore autoantibodies in the serum of CA patients. As a result, anti-transcobalamin receptor (TCblR) antibodies (Abs) were specifically detected in 24% of CA patients. Patients with positive anti-TCblR Abs were spared from peripheral neuropathy compared to those with negative anti-TCblR Abs, showing characteristics as CA confined to the skin. In addition, we revealed that anti-TCblR Abs trigger the autocrine loop of interleukin-6 mediated by tripartite motif-containing protein 21 in human endothelial cells and induce periarterial inflammation in murine skin. Furthermore, we demonstrated that methylcobalamin, a ligand of TCblR, ameliorates inflammation caused by anti-TCblR Abs both in vitro and in vivo. Collectively, our investigation unveils the pathologic significance of anti-TCblR Abs in CA and their potential as a diagnostic marker and a pathophysiology-oriented therapeutic target.
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Affiliation(s)
- Kazuki M Matsuda
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Hirohito Kotani
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kei Yamaguchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan; ProteoBridge Corporation, Tokyo, Japan
| | - Taishi Okumura
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan; ProteoBridge Corporation, Tokyo, Japan
| | - Eriko Fukuda
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Masanori Kono
- Department of Allergy and Rheumatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Teruyoshi Hisamoto
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Ruriko Kawanabe
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Yuta Norimatsu
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Ai Kuzumi
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Maiko Fukayama
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Takemichi Fukasawa
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Satoshi Ebata
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Asako Yoshizaki-Ogawa
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan; ProteoBridge Corporation, Tokyo, Japan
| | - Shinichi Sato
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan.
| | - Ayumi Yoshizaki
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan.
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Kumar A, Fitoussi N, Sanadhya P, Sichov N, Bucki P, Bornstein M, Belausuv E, Brown Miyara S. Two Candidate Meloidogyne javanica Effector Genes, MjShKT and MjPUT3: A Functional Investigation of Their Roles in Regulating Nematode Parasitism. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:79-94. [PMID: 36324054 DOI: 10.1094/mpmi-10-22-0212-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
During parasitism, root-knot nematode Meloidogyne spp. inject molecules termed effectors that have multifunctional roles in construction and maintenance of nematode feeding sites. As an outcome of transcriptomic analysis of Meloidogyne javanica, we identified and characterized two differentially expressed genes encoding the predicted proteins MjShKT, carrying a Stichodactyla toxin (ShKT) domain, and MjPUT3, carrying a ground-like domain, both expressed during nematode parasitism of the tomato plant. Fluorescence in-situ hybridization revealed expression of MjShKT and MjPUT3 in the dorsal esophageal glands, suggesting their injection into host cells. MjShKT expression was upregulated during the parasitic life stages, to a maximum at the mature female stage, whereas MjPUT3 expression increased in third- to fourth-stage juveniles. Subcellular in-planta localization of MjShKT and MjPUT3 using a fused fluorescence marker indicated MjShKT co-occurrence with the endoplasmic reticulum, the perinuclear endoplasmatic reticulum, and the Golgi organelle markers, while MjPUT3 localized, to some extent, within the endoplasmatic reticulum and was clearly observed within the nucleoplasm. MjShKT inhibited programmed cell death induced by overexpression of MAPKKKα and Gpa2/RBP-1. Overexpression of MjShKT in tomato hairy roots allowed an increase in nematode reproduction, as indicated by the high number of eggs produced on roots overexpressing MjShKT. Roots overexpressing MjPUT3 were characterized by enhanced root growth, with no effect on nematode development on those roots. Investigation of the two candidate effectors suggested that MjShKT is mainly involved in manipulating the plant effector-triggered immune response toward establishment and maintenance of active feeding sites, whereas MjPUT3 might modulate roots morphology in favor of nematode fitness in the host roots. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Anil Kumar
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
| | - Nathalia Fitoussi
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Payal Sanadhya
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
| | - Natalia Sichov
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
| | - Patricia Bucki
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
| | - Menachem Bornstein
- Department of Plant Pathology and Weed Research, ARO, Volcani Center, Bet Dagan 50250, Israel
| | - Eduard Belausuv
- Department of Plant Sciences, ARO, Volcani Center, Bet Dagan 50250, Israel
| | - Sigal Brown Miyara
- Department of Entomology, Nematology and Chemistry units, Agricultural Research Organization (ARO), Volcani Center, Bet Dagan 50250, Israel
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10
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Nishiguchi R, Tanaka T, Hayashida J, Nakagita T, Zhou W, Takeda H. Evaluation of Cell-Free Synthesized Human Channel Proteins for In Vitro Channel Research. MEMBRANES 2022; 13:48. [PMID: 36676855 PMCID: PMC9861611 DOI: 10.3390/membranes13010048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Despite channel proteins being important drug targets, studies on channel proteins remain limited, as the proteins are difficult to express and require correct complex formation within membranes. Although several in vitro synthesized recombinant channels have been reported, considering the vast diversity of the structures and functions of channel proteins, it remains unclear which classes of channels cell-free synthesis can be applied to. In this study, we synthesized 250 clones of human channels, including ion channel pore-forming subunits, gap junction proteins, porins, and regulatory subunits, using a wheat cell-free membrane protein production system, and evaluated their synthetic efficiency and function. Western blotting confirmed that 95% of the channels were successfully synthesized, including very large channels with molecular weights of over 200 kDa. A subset of 47 voltage-gated potassium ion channels was further analyzed using a planar lipid bilayer assay, out of which 80% displayed a voltage-dependent opening in the assay. We co-synthesized KCNB1 and KCNS3, a known heteromeric complex pair, and demonstrated that these channels interact on a liposome. These results indicate that cell-free protein synthesis provides a promising solution for channel studies to overcome the bottleneck of in vitro protein production.
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Affiliation(s)
- Rei Nishiguchi
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Toyohisa Tanaka
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Jun Hayashida
- Nissan Chemical Corporation, Shiraoka 1470, Shiraoka 349-0294, Saitama, Japan
| | - Tomoya Nakagita
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Wei Zhou
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Hiroyuki Takeda
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
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11
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Cui Z, Chen P, Li C, Deng S, Yang H. Chip-DSF: A rapid screening strategy for drug protein targets. Pharmacol Res 2022; 182:106346. [PMID: 35809766 DOI: 10.1016/j.phrs.2022.106346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/12/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022]
Abstract
Identification of the drug target of lead compounds is an important means for rapid and efficient drug discovery. Protein chips are a high-throughput protein function analysis technology that has been widely used in screening drug protein targets in recent years. However, the verification of the results after high-throughput protein chip screening is still cumbersome. Based on our mature protein chip preparation platform, we prepared a protein chip containing 150 important high-frequency protein targets and used antibodies to prove the availability of the protein chip. To improve the accuracy of target screening, we combined the label-free differential scanning fluorimetry (DSF) with the protein chip, proposing the Chip-DSF strategy. Subsequently, we tested the method with small molecular ginsenoside-Rg2 (Rg2). The Chip-DSF strategy was used to successfully screen the potential target protein KRAS(G12C) of Rg2. Consistently, we found that Rg2 could inhibit NCI-H23 cell proliferation by inducing cell cycle arrest. Also, we found that Rg2 could reduce the amount of KRAS protein and inhibit the phosphorylation of KRAS downstream key signaling protein ERK1, RPS6, and P70S6K in NCI-H23 cells. Collectively, our Chip-DSF strategy could achieve rapid target verification which improved the accuracy and efficiency of target screening of protein chips.
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Affiliation(s)
- Zhao Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Peng Chen
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China; Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Caifeng Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China; Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shiwen Deng
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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12
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CF-PPiD technology based on cell-free protein array and proximity biotinylation enzyme for in vitro direct interactome analysis. Sci Rep 2022; 12:10592. [PMID: 35732899 PMCID: PMC9217950 DOI: 10.1038/s41598-022-14872-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
Protein–protein interaction (PPI) analysis is a key process to understand protein functions. Recently, we constructed a human protein array (20 K human protein beads array) consisting of 19,712 recombinant human proteins produced by a wheat cell-free protein production system. Here, we developed a cell-free protein array technology for proximity biotinylation-based PPI identification (CF-PPiD). The proximity biotinylation enzyme AirID-fused TP53 and -IκBα proteins each biotinylated specific interacting proteins on a 1536-well magnetic plate. In addition, AirID-fused cereblon was shown to have drug-inducible PPIs using CF-PPiD. Using the human protein beads array with AirID-IκBα, 132 proteins were biotinylated, and then selected clones showed these biological interactions in cells. Although ZBTB9 was not immunoprecipitated, it was highly biotinylated by AirID-IκBα, suggesting that this system detected weak interactions. These results indicated that CF-PPiD is useful for the biochemical identification of directly interacting proteins.
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13
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Matsuda KM, Yoshizaki A, Yamaguchi K, Fukuda E, Okumura T, Ogawa K, Ono C, Norimatsu Y, Kotani H, Hisamoto T, Kawanabe R, Kuzumi A, Fukasawa T, Ebata S, Miyagawa T, Yoshizaki-Ogawa A, Goshima N, Sato S. Autoantibody Landscape Revealed by Wet Protein Array: Sum of Autoantibody Levels Reflects Disease Status. Front Immunol 2022; 13:893086. [PMID: 35603173 PMCID: PMC9114879 DOI: 10.3389/fimmu.2022.893086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Autoantibodies are found in various pathological conditions such as autoimmune diseases, infectious diseases, and malignant tumors. However their clinical implications have not yet been fully elucidated. Herein, we conducted proteome-wide autoantibody screening and quantification with wet protein arrays consisting of proteins synthesized from proteome-wide human cDNA library (HuPEX) maintaining their three-dimensional structure. A total of 565 autoantibodies were identified from the sera of three representative inflammatory disorders (systemic sclerosis, psoriasis, and cutaneous arteritis). Each autoantibody level either positively or negatively correlated with serum levels of C-reactive protein, the best-recognized indicator of inflammation. In particular, we discovered total levels of a subset of autoantibodies correlates with the severity of clinical symptoms. From the sera of malignant melanoma, 488 autoantibodies were detected. Notably, patients with metastases had increased overall autoantibody production compared to those with tumors limiting to the primary site. Collectively, proteome-wide screening of autoantibodies using the in vitro proteome can reveal the "autoantibody landscape" of human subjects and may provide novel clinical biomarkers.
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Affiliation(s)
- Kazuki M Matsuda
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Ayumi Yoshizaki
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kei Yamaguchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,ProteoBridge Corporation, Tokyo, Japan
| | - Eriko Fukuda
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Taishi Okumura
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,ProteoBridge Corporation, Tokyo, Japan
| | - Koji Ogawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,ProteoBridge Corporation, Tokyo, Japan
| | - Chihiro Ono
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,ProteoBridge Corporation, Tokyo, Japan
| | - Yuta Norimatsu
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Hirohito Kotani
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Teruyoshi Hisamoto
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Ruriko Kawanabe
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Ai Kuzumi
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Takemichi Fukasawa
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Satoshi Ebata
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Takuya Miyagawa
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Asako Yoshizaki-Ogawa
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,ProteoBridge Corporation, Tokyo, Japan
| | - Shinichi Sato
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
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14
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Hirano S, Matsumoto K, Tanaka K, Amano N, Koguchi D, Ikeda M, Shimizu Y, Tsuchiya B, Nagashio R, Sato Y, Iwamura M. DJ-1 Expression Might Serve as a Biologic Marker in Patients with Bladder Cancer. Cancers (Basel) 2022; 14:2535. [PMID: 35626138 PMCID: PMC9139869 DOI: 10.3390/cancers14102535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 02/03/2023] Open
Abstract
The overexpression of DJ-1 protein and its secretion into the bloodstream has been reported in various neoplasms. However, serum levels and the subcellular localization of DJ-1 have not been analyzed in detail in bladder cancer (BC). Our comprehensive analysis of these variables started with the measurement of DJ-1 in serum from 172 patients with BC, 20 patients with urolithiasis and 100 healthy participants. Next, an immunohistochemical study of DJ-1 expression and localization was conducted in 92 patients with BC, and associations with clinicopathologic factors and patient outcomes were evaluated. Serum DJ-1 was significantly higher in patients with BC than in those with urolithiasis or in healthy participants. Immunohistochemically, a cytoplasm-positive (Cy+) and nucleus-negative (N-) DJ-1 pattern was associated with age and pathologic stage. Log-rank tests indicated that the Cy+, N- pattern was significantly associated with overall survival (OS), recurrence-free survival (RFS), and cancer specific survival (CSS). In addition, the Cy+, N- pattern was an independent prognostic factor in the multivariate analysis adjusted for the effects of the clinicopathologic outcomes. The investigation of DJ-1 expression might help physicians to make decisions regarding further follow-up and additional treatments.
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Affiliation(s)
- Shuhei Hirano
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Kazumasa Matsumoto
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Kei Tanaka
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (K.T.); (B.T.); (R.N.)
- Department of Pathology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Noriyuki Amano
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Dai Koguchi
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Masaomi Ikeda
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Yuriko Shimizu
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
| | - Benio Tsuchiya
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (K.T.); (B.T.); (R.N.)
| | - Ryo Nagashio
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (K.T.); (B.T.); (R.N.)
| | - Yuichi Sato
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
- Department of Applied Tumor Pathology, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (K.T.); (B.T.); (R.N.)
| | - Masatsugu Iwamura
- Department of Urology, School of Medicine, Graduate School of Medical Sciences, Kitasato University, Sagamihara 252-0374, Japan; (S.H.); (N.A.); (D.K.); (M.I.); (Y.S.); (Y.S.); (M.I.)
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15
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Keown RA, Dums JT, Brumm PJ, MacDonald J, Mead DA, Ferrell BD, Moore RM, Harrison AO, Polson SW, Wommack KE. Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes. Front Microbiol 2022; 13:858366. [PMID: 35531281 PMCID: PMC9069017 DOI: 10.3389/fmicb.2022.858366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/08/2022] [Indexed: 01/21/2023] Open
Abstract
Viruses are the most abundant and diverse biological entities on the planet and constitute a significant proportion of Earth's genetic diversity. Most of this diversity is not represented by isolated viral-host systems and has only been observed through sequencing of viral metagenomes (viromes) from environmental samples. Viromes provide snapshots of viral genetic potential, and a wealth of information on viral community ecology. These data also provide opportunities for exploring the biochemistry of novel viral enzymes. The in vitro biochemical characteristics of novel viral DNA polymerases were explored, testing hypothesized differences in polymerase biochemistry according to protein sequence phylogeny. Forty-eight viral DNA Polymerase I (PolA) proteins from estuarine viromes, hot spring metagenomes, and reference viruses, encompassing a broad representation of currently known diversity, were synthesized, expressed, and purified. Novel functionality was shown in multiple PolAs. Intriguingly, some of the estuarine viral polymerases demonstrated moderate to strong innate DNA strand displacement activity at high enzyme concentration. Strand-displacing polymerases have important technological applications where isothermal reactions are desirable. Bioinformatic investigation of genes neighboring these strand displacing polymerases found associations with SNF2 helicase-associated proteins. The specific function of SNF2 family enzymes is unknown for prokaryotes and viruses. In eukaryotes, SNF2 enzymes have chromatin remodeling functions but do not separate nucleic acid strands. This suggests the strand separation function may be fulfilled by the DNA polymerase for viruses carrying SNF2 helicase-associated proteins. Biochemical data elucidated from this study expands understanding of the biology and ecological behavior of unknown viruses. Moreover, given the numerous biotechnological applications of viral DNA polymerases, novel viral polymerases discovered within viromes may be a rich source of biological material for further in vitro DNA amplification advancements.
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Affiliation(s)
- Rachel A. Keown
- Department of Biological Sciences, College of Arts and Sciences, University of Delaware, Newark, DE, United States
| | - Jacob T. Dums
- Biotechnology Program, North Carolina State University, Raleigh, NC, United States
| | | | | | - David A. Mead
- Varigen Biosciences Corporation, Middleton, WI, United States
| | - Barbra D. Ferrell
- Department of Plant and Soil Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, United States
| | - Ryan M. Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Amelia O. Harrison
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
- Department of Computer and Information Sciences, College of Arts and Sciences, University of Delaware, Newark, DE, United States
| | - K. Eric Wommack
- Department of Plant and Soil Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, United States
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16
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Harada N, Arahori Y, Okuyama M, Luis PB, Joseph AI, Kitakaze T, Goshima N, Schneider C, Inui H, Yamaji R. Curcumin activates G protein-coupled receptor 97 (GPR97) in a manner different from glucocorticoid. Biochem Biophys Res Commun 2022; 595:41-46. [DOI: 10.1016/j.bbrc.2022.01.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
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17
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Identification of G protein-coupled receptor 55 (GPR55) as a target of curcumin. NPJ Sci Food 2022; 6:4. [PMID: 35031622 PMCID: PMC8760322 DOI: 10.1038/s41538-021-00119-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/13/2021] [Indexed: 12/22/2022] Open
Abstract
The identification of molecular targets of bioactive food components is important to understand the mechanistic aspect of their physiological functions. Here, we have developed a screening system that enables us to determine the activation of G protein-coupled receptors (GPCRs) by food components and have identified GPR55 as a target for curcumin. Curcumin activated GPR55 and induced serum-response element- and serum-response factor-mediated transcription, which were inhibited by Rho kinase and GPR55 antagonists. Both the methoxy group and the heptadienone moiety of curcumin were required for GPR55 activation. The F1905.47 residue of GPR55 was important for the interaction with curcumin. The curcumin-induced secretion of glucagon-like peptide-1 in GLUTag cells was inhibited by a GPR55 antagonist. These results indicate that expression screening is a useful system to identify GPCRs as targets of food components and strongly suggest that curcumin activates GPR55 as an agonist, which is involved in the physiological function of curcumin.
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18
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Manteca A, Gadea A, Van Assche D, Cossard P, Gillard-Bocquet M, Beneyton T, Innis CA, Baret JC. Directed Evolution in Drops: Molecular Aspects and Applications. ACS Synth Biol 2021; 10:2772-2783. [PMID: 34677942 PMCID: PMC8609573 DOI: 10.1021/acssynbio.1c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 11/29/2022]
Abstract
The process of optimizing the properties of biological molecules is paramount for many industrial and medical applications. Directed evolution is a powerful technique for modifying and improving biomolecules such as proteins or nucleic acids (DNA or RNA). Mimicking the mechanism of natural evolution, one can enhance a desired property by applying a suitable selection pressure and sorting improved variants. Droplet-based microfluidic systems offer a high-throughput solution to this approach by helping to overcome the limiting screening steps and allowing the analysis of variants within increasingly complex libraries. Here, we review cases where successful evolution of biomolecules was achieved using droplet-based microfluidics, focusing on the molecular processes involved and the incorporation of microfluidics to the workflow. We highlight the advantages and limitations of these microfluidic systems compared to low-throughput methods and show how the integration of these systems into directed evolution workflows can open new avenues to discover or improve biomolecules according to user-defined conditions.
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Affiliation(s)
- Aitor Manteca
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Alejandra Gadea
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | | | - Pauline Cossard
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Mélanie Gillard-Bocquet
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Thomas Beneyton
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
| | - C. Axel Innis
- Univ.
Bordeaux, Institut National de la Santé et de la Recherche
Médicale, Centre National de la Recherche Scientifique, ARNA,
U1212, UMR 5320, Institut Européen de Chimie et Biologie, F-33600 Pessac, France
| | - Jean-Christophe Baret
- Univ.
Bordeaux, CNRS, CRPP, UMR 5031, F-33610, Pessac, France
- Institut
Universitaire de France, F-75231 Paris, France
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19
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A chalcone derivative suppresses TSLP induction in mice and human keratinocytes through binding to BET family proteins. Biochem Pharmacol 2021; 194:114819. [PMID: 34757034 DOI: 10.1016/j.bcp.2021.114819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/23/2022]
Abstract
Although treatments for allergic diseases have improved, side effects and treatment resistance remain as challenges. New therapeutic drugs for allergic diseases are urgently required. Thymic stromal lymphopoietin (TSLP) is a cytokine target for prevention and treatment of allergic diseases. Since TSLP is produced from epithelial cells in allergic diseases, TSLP inhibitors may be new anti-allergic drugs. We previously identified a new inhibitor of TSLP production, named 16D10. However, its target of action remained unclarified. In this study, we found proteins binding to 16D10 from 24,000 human protein arrays by AlphaScreen-based high-throughput screening and identified bromodomain and extra-terminal (BET) family proteins as targets. We also clarified the detailed mode of interaction between 16D10 and a BET family protein using X-ray crystallography. Furthermore, we confirmed that inhibitors of BET family proteins suppressed TSLP induction and IL-33 and IL-36γ expression in both mouse and human keratinocyte cell lines. Taken together, our findings suggest that BET family proteins are involved in the suppression of TSLP production by 16D10. These proteins can contribute to the pathology of atopic dermatitis via TSLP regulation in keratinocytes and have potential as therapeutic targets in allergic diseases.
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20
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Fukuda E, Tanaka H, Yamaguchi K, Takasaka M, Kawamura Y, Okuda H, Isotani A, Ikawa M, Shapiro VS, Tsuchida J, Okada Y, Tsujimura A, Miyagawa Y, Fukuhara S, Kawakami Y, Wada M, Nishimune Y, Goshima N. Identification and characterization of the antigen recognized by the germ cell mAb TRA98 using a human comprehensive wet protein array. Genes Cells 2021; 26:180-189. [PMID: 33527666 DOI: 10.1111/gtc.12832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022]
Abstract
TRA98 is a rat monoclonal antibody (mAb) which recognizes a specific antigen in the nuclei of germ cells. mAb TRA98 has been used to understand the mechanism of germ cell development and differentiation in many studies. In mice, the antigen recognized by mAb TRA98 or GCNA1 has been reported to be a GCNA gene product, but despite the demonstration of the immunoreactivity of this mAb in human testis and sperm in 1997, the antigen in humans remains unknown, as of date. To identify the human antigen recognized by mAb TRA98, a human comprehensive wet protein array was developed containing 19,446 proteins derived from human cDNAs. Using this array, it was found that the antigen of mAb TRA98 is not a GCNA gene product, but nuclear factor-κB activating protein (NKAP). In mice, mAb TRA98 recognized both the GCNA gene product and NKAP. Furthermore, conditional knockout of Nkap in mice revealed a phenotype of Sertoli cell-only syndrome. Although NKAP is a ubiquitously expressed protein, NKAP recognized by mAb TRA98 in mouse testis was SUMOylated. These results suggest that NKAP undergoes modifications, such as SUMOylation in the testis, and plays an important role in spermatogenesis.
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Affiliation(s)
- Eriko Fukuda
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Hiromitsu Tanaka
- Molecular Biology Division, Faculty of Pharmaceutical Sciences, Nagasaki International University, Nagasaki, Japan
| | - Kei Yamaguchi
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Mieko Takasaka
- Japan Biological Informatics Consortium (JBIC), Tokyo, Japan
| | | | - Hidenobu Okuda
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ayako Isotani
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | - Junji Tsuchida
- Department of Science for Laboratory Animal Experimentation, Research Institute for Microbial Disease, Osaka University, Osaka, Japan
| | - Yuki Okada
- Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | - Akira Tsujimura
- Department of Urology, Juntendo University Urayasu Hospital, Urayasu, Chiba, Japan
| | - Yasushi Miyagawa
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinichiro Fukuhara
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Kawakami
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Morimasa Wada
- Molecular Biology Division, Faculty of Pharmaceutical Sciences, Nagasaki International University, Nagasaki, Japan
| | - Yoshitake Nishimune
- Department of Science for Laboratory Animal Experimentation, Research Institute for Microbial Disease, Osaka University, Osaka, Japan
| | - Naoki Goshima
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.,Department of Human Sciences, Faculty of Human Sciences, Musasino University, Tokyo, Japan
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21
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Kagiwada H, Kiboku T, Matsuo H, Kitazawa M, Fukui K, Horimoto K. Assessing the activation/inhibition of tyrosine kinase-related pathways with a newly developed platform. Proteomics 2021; 21:e2000251. [PMID: 34151541 DOI: 10.1002/pmic.202000251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/21/2022]
Abstract
The phosphorylation of cellular proteins plays a crucial role in the transduction of various signals from outside the cell into the nucleus. The signals are transduced by phosphorylation chain reactions within multiple pathways; however, determining which pathways are responsible for each defined signal has proven challenging. To estimate the activity of each pathway, we developed a phosphorylation array platform comprising a protein array with 1200 proteins belonging to 376 signalling pathways and an analytical method to estimate pathway activity based on the phosphorylation levels of proteins. The performance of our system was assessed by reconstructing kinase-substrate relationships, as well as by estimating pathway activity upon epidermal growth factor (EGF) stimulation and the pharmacological inhibition of epidermal growth factor receptor (EGFR). As a result, kinase-substrate relationships were reliably reconstructed based on the precise measurement of phosphorylation levels of constituent proteins on the array. Furthermore, the pathway activities associated with EGF stimulation and EGFR inhibition were successfully traced through the related pathways from the outer membrane to the nucleus along a time course. Thus, our phosphorylation array system can effectively assess the activity of specific signalling pathways that are perturbed by extracellular stimuli, such as various drugs.
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Affiliation(s)
- Harumi Kagiwada
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Kotu-ku, Tokyo, Japan
| | | | | | | | - Kazuhiko Fukui
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Kotu-ku, Tokyo, Japan
| | - Katsuhisa Horimoto
- Socium Inc., Tokyo, Japan.,Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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22
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Yamaoka Y, Miyakawa K, Jeremiah SS, Funabashi R, Okudela K, Kikuchi S, Katada J, Wada A, Takei T, Nishi M, Shimizu K, Ozawa H, Usuku S, Kawakami C, Tanaka N, Morita T, Hayashi H, Mitsui H, Suzuki K, Aizawa D, Yoshimura Y, Miyazaki T, Yamazaki E, Suzuki T, Kimura H, Shimizu H, Okabe N, Hasegawa H, Ryo A. Highly specific monoclonal antibodies and epitope identification against SARS-CoV-2 nucleocapsid protein for antigen detection tests. Cell Rep Med 2021; 2:100311. [PMID: 34027498 PMCID: PMC8126173 DOI: 10.1016/j.xcrm.2021.100311] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/02/2021] [Accepted: 05/13/2021] [Indexed: 12/24/2022]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic is a major global public health concern. Although rapid point-of-care testing for detecting viral antigen is important for management of the outbreak, the current antigen tests are less sensitive than nucleic acid testing. In our current study, we produce monoclonal antibodies (mAbs) that exclusively react with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and exhibit no cross-reactivity with other human coronaviruses, including SARS-CoV. Molecular modeling suggests that the mAbs bind to epitopes present on the exterior surface of the nucleocapsid, making them suitable for detecting SARS-CoV-2 in clinical samples. We further select the optimal pair of anti-SARS-CoV-2 nucleocapsid protein (NP) mAbs using ELISA and then use this mAb pair to develop immunochromatographic assay augmented with silver amplification technology. Our mAbs recognize the variants of concern (501Y.V1-V3) that are currently in circulation. Because of their high performance, the mAbs of this study can serve as good candidates for developing antigen detection kits for COVID-19.
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Affiliation(s)
- Yutaro Yamaoka
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Isehara, Kanagawa 259-1146, Japan
| | - Kei Miyakawa
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | | | - Rikako Funabashi
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Koji Okudela
- Department of Pathology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Sayaka Kikuchi
- Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Isehara, Kanagawa 259-1146, Japan
| | - Junichi Katada
- Medical Systems Research & Development Center, FUJIFILM Corporation, Kaisei, Kanagawa 258-8538, Japan
| | - Atsuhiko Wada
- Medical Systems Research & Development Center, FUJIFILM Corporation, Kaisei, Kanagawa 258-8538, Japan
| | - Toshiki Takei
- Medical Systems Research & Development Center, FUJIFILM Corporation, Kaisei, Kanagawa 258-8538, Japan
| | - Mayuko Nishi
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kohei Shimizu
- Yokohama City Institute of Public Health, Yokohama, Kanagawa 236-0051, Japan
| | - Hiroki Ozawa
- Yokohama City Institute of Public Health, Yokohama, Kanagawa 236-0051, Japan
| | - Shuzo Usuku
- Yokohama City Institute of Public Health, Yokohama, Kanagawa 236-0051, Japan
| | - Chiharu Kawakami
- Yokohama City Institute of Public Health, Yokohama, Kanagawa 236-0051, Japan
| | - Nobuko Tanaka
- Yokohama City Institute of Public Health, Yokohama, Kanagawa 236-0051, Japan
| | - Takeshi Morita
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Hiroyuki Hayashi
- Division of Pathology, Yokohama Municipal Citizen’s Hospital, Yokohama, Kanagawa 221-0855, Japan
| | - Hideaki Mitsui
- Department of Pathology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Keita Suzuki
- Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Isehara, Kanagawa 259-1146, Japan
| | - Daisuke Aizawa
- Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Isehara, Kanagawa 259-1146, Japan
| | - Yukihiro Yoshimura
- Division of Infectious Disease, Yokohama Municipal Citizen’s Hospital, Yokohama, Kanagawa 221-0855, Japan
| | - Tomoyuki Miyazaki
- Department of Physiology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Etsuko Yamazaki
- Clinical Laboratory Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Hirokazu Kimura
- School of Medical Technology, Faculty of Health Sciences, Gunma Paz University, Takasaki, Gunma 370-0006, Japan
| | - Hideaki Shimizu
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Kanagawa 210-0821, Japan
| | - Nobuhiko Okabe
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Kanagawa 210-0821, Japan
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan
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23
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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24
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Berselli A, Ramos MJ, Menziani MC. Novel Pet-Degrading Enzymes: Structure-Function from a Computational Perspective. Chembiochem 2021; 22:2032-2050. [PMID: 33470503 DOI: 10.1002/cbic.202000841] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/19/2021] [Indexed: 12/12/2022]
Abstract
The bacterium strain Ideonella sakaiensis 201-F6 is able to hydrolyze low-crystallinity PET films at 30 °C due to two enzymes named PETase and MHETase. Since its discovery, many efforts have been dedicated to elucidating the structure and features of those two enzymes, and various authors have highlighted the necessity to optimize both the substrate binding site and the global structure in order to enhance the stability and catalytic activity of these PET biocatalysts so as to make them more suitable for industrial applications. In this review, the strategies adopted by different research groups to investigate the structure and functionality of both PETase and MHETase in depth are described, emphasizing the advantages provided by the use of computational methods to complement and drive experiments. Subsequently, the modifications implemented with protein engineering are discussed. The versatility of the enzymes secreted by I. sakaiensis enables the prediction that they will find several applications in the disposal of PET debris, encouraging a prioritization of efforts in this prolific research field.
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Affiliation(s)
- Alessandro Berselli
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Maria J Ramos
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
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25
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A Relationship between NTP and Cell Extract Concentration for Cell-Free Protein Expression. Life (Basel) 2021; 11:life11030237. [PMID: 33805612 PMCID: PMC7999496 DOI: 10.3390/life11030237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/29/2023] Open
Abstract
The cell-free protein synthesis (CFPS) that synthesizes mRNA and protein from a template DNA has been featured as an important tool to emulate living systems in vitro. However, an obstacle to emulate living cells by CFPS is the loss of activity in the case of usage of high concentration cell extracts. In this study, we found that a high concentration of NTP which inhibits in the case of lower concentration cell extract restored the loss of CFPS activity using high concentration cell extracts. The NTP restoration was independent of the energy regeneration system used, and NTP derivatives also restored the levels of CFPS using a high concentration cell extract. Experiments using dialysis mode of CFPS showed that continuous exchange of small molecule reduced levels of NTP requirement and improved reaction speed of CFPS using the high concentration of cell extract. These findings contribute to the development of a method to understand the condition of living cells by in vitro emulation, and are expected to lead to the achievement of the reconstitution of living cells from biomolecule mixtures.
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26
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Michigami M, Takahashi K, Yamashita H, Ye Z, Nakase I, Fujii I. A "ligand-targeting" peptide-drug conjugate: Targeted intracellular drug delivery by VEGF-binding helix-loop-helix peptides via receptor-mediated endocytosis. PLoS One 2021; 16:e0247045. [PMID: 33630870 PMCID: PMC7906330 DOI: 10.1371/journal.pone.0247045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/29/2021] [Indexed: 12/27/2022] Open
Abstract
As a new alternative to antibody-drug conjugates, we generated “ligand-targeting” peptide-drug conjugates (PDCs), which utilize receptor-mediated endocytosis for targeted intracellular drug delivery. The PDC makes a complex with an extracellular ligand and then binds to the receptor on the cell surface to stimulate intracellular uptake via the endocytic pathway. A helix-loop-helix (HLH) peptide was designed as the drug carrier and randomized to give a conformationally constrained peptide library. The phage-displayed library was screened against vascular endothelial growth factor (VEGF) to yield the binding peptide M49, which exhibited strong binding affinity (KD = 0.87 nM). The confocal fluorescence microscopy revealed that peptide M49 formed a ternary complex with VEGF and its receptor, which was then internalized into human umbilical vein endothelial cells (HUVECs) via VEGF receptor-mediated endocytosis. The backbone-cyclized peptide M49K was conjugated with a drug, monomethyl auristatin E, to afford a PDC, which inhibited VEGF-induced HUVEC proliferation. HLH peptides and their PDCs have great potential as a new modality for targeted molecular therapy.
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Affiliation(s)
- Masataka Michigami
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Kentaro Takahashi
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Haruna Yamashita
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | | | - Ikuhiko Nakase
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Ikuo Fujii
- Department of Biological Science, Osaka Prefecture University, Sakai, Osaka, Japan
- * E-mail:
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27
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ENDO Y. Development of a cell-free protein synthesis system for practical use. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:261-276. [PMID: 33980755 PMCID: PMC8141837 DOI: 10.2183/pjab.97.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Conventional cell-free protein synthesis systems had been the major platform to study the mechanism behind translating genetic information into proteins, as proven in the central dogma of molecular biology. Albeit being powerful research tools, most of the in vitro methods at the time failed to produce enough protein for practical use. Tremendous efforts were being made to overcome the limitations of in vitro translation systems, though mostly with limited success. While great knowledge was accumulated on the translation mechanism and ribosome structure, researchers rationalized that it may be impossible to fully reconstitute such a complex molecular process in a test tube. This review will examine how we have solved the difficulties holding back progress. Our newly developed cell-free protein synthesis system is based on wheat embryos and has many excellent characteristics, in addition to its high translation activity and robustness. Combined with other novel elementary technologies, we have established cell-free protein synthesis systems for practical use in research and applied sciences.
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Affiliation(s)
- Yaeta ENDO
- Ehime Prefectural University of Health Sciences, Tobe-cho, Iyo-gun, Ehime, Japan
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28
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Okimune KI, Nagy SK, Hataya S, Endo Y, Takasuka TE. Reconstitution of Drosophila and human chromatins by wheat germ cell-free co-expression system. BMC Biotechnol 2020; 20:62. [PMID: 33261588 PMCID: PMC7708258 DOI: 10.1186/s12896-020-00655-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Elaboration of the epigenetic regulation of chromatin is a long-standing aim in molecular and cellular biology. Hence, there is a great demand for the development of in vitro methods to reconstitute chromatin that can be used directly for biochemical assays. The widely used wheat germ cell-free protein expression method provides broad applications to investigate the function and structure of eukaryotic proteins. Such advantages, including high translation efficiency, flexibility, and possible automatization, are beneficial for achieving native-like chromatin substrates for in vitro studies. RESULTS We describe a novel, single-step in vitro chromatin assembly method by using the wheat germ cell-free protein synthesis. We demonstrated that both Drosophila and human chromatins can be reconstituted in the course of the in vitro translation of core histones by the addition of chromatin assembly factors, circular plasmid, and topoisomerase I in an ATP-dependent manner. Drosophila chromatin assembly was performed in 4 h at 26 °C, in the presence of premixed mRNAs encoding the core histones, dAcf1/dISWI chromatin remodeling complex, and nucleosome assembly protein, dNAP1. Similarly, the human chromatin was assembled by co-expressing the human core histones with Drosophila chromatin remodeling factor, dISWI, and chromatin chaperone, dNLP, for 6 h at 26 °C. The presence of reconstituted chromatin was monitored by DNA supercoiling assay, also the regular spacing of nucleosomes was assessed by Micrococcal nuclease assay. Furthermore, Drosophila linker histone H1-containing chromatin was reconstituted, affirming that the in vitro assembled chromatin is suitable for downstream applications. CONCLUSIONS The method described in this study allows the assembly of Drosophila and human chromatins, possibly in native-like form, by using a wheat germ cell-free protein expression. Although both chromatins were reconstituted successfully, there were unexpected differences with respect to the required ratio of histone-coding mRNAs and the reaction time. Overall, our new in vitro chromatin reconstitution method will aid to characterize the unrevealed structure, function, and regulation of chromatin dynamics.
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Affiliation(s)
- Kei-Ichi Okimune
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
| | - Szilvia K Nagy
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Shogo Hataya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yaeta Endo
- Proteo-Science Center of Ehime University, Matsuyama, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan. .,Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan. .,GI-CORE, Hokkaido University, Sapporo, 060-8589, Japan.
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29
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Weber J, Braun CJ, Saur D, Rad R. In vivo functional screening for systems-level integrative cancer genomics. Nat Rev Cancer 2020; 20:573-593. [PMID: 32636489 DOI: 10.1038/s41568-020-0275-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Herein, we review functional screening strategies in mice using genetic perturbation and chemical mutagenesis. We outline the spectrum of genetic tools that exist, such as transposons, CRISPR and RNAi and describe discoveries emerging from their use. Genome-wide or targeted screens are being used to uncover genomic and regulatory landscapes in oncogenesis, metastasis or drug resistance. Versatile screening systems support experimentation in diverse genetic and spatio-temporal settings to integrate molecular, cellular or environmental context-dependencies. We also review the combination of in vivo screening and barcoding strategies to study genetic interactions and quantitative cancer dynamics during tumour evolution. These scalable functional genomics approaches are transforming our ability to interrogate complex biological systems.
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Affiliation(s)
- Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany.
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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30
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Zhang J, Zeng Y, Liu B, Deng X. MerP/MerT-mediated mechanism: A different approach to mercury resistance and bioaccumulation by marine bacteria. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:122062. [PMID: 31955028 DOI: 10.1016/j.jhazmat.2020.122062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 06/10/2023]
Abstract
Currently, mechanism underlying mercury resistance and bioaccumulation of marine bacteria remains little understood. A marine bacterium Pseudomonas pseudoalcaligenes S1 is resistant to 120 mg/L Hg2+ with bioaccumulation capacity of 133.33 mg/g. Accordingly, Hg2+ resistance and bioaccumulation mechanism of S1 was investigated at molecular and cellular level. Annotation of S1 transcriptome reveals 772 differentially expressed genes, including Hg2+-relevant genes merT, merP and merA. Both merT and merP gene have three complete copies in S1 genome, while merA gene has only one. In order to evaluate the function of these Hg2+-relevant genes, three recombinant strains were constructed to express MerA (named as A), MerT/MerP (TP) and MerT/MerP/MerA (TPA), respectively. The results show that Hg2+ resistance of strain TP, TPA, and A are improved with minimum inhibition concentration (MIC) being 60 mg/L, 40 mg/L, and 20 mg/L, respectively compared to 2 mg/L of host strain. Strain TP and TPA exhibit enhanced Hg2+ bioaccumulation capacity, while strain A does not differ from the control. Their equilibrium Hg2+ bioaccumulation capacities are 110.48 mg/g, 94.49 mg/g, 83.76 mg/g and 82.29 mg/g, respectively. Summarily, different from most microorganisms that exhibit Hg2+ resistance by MerA-mediated mechanism, marine bacterium S1 achieves Hg2+ resistance and bioaccumulation capability via MerT/MerP-mediated strategy.
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Affiliation(s)
- Jinlong Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yiting Zeng
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Bing Liu
- School of Traffic and Environment, Shenzhen Institute of Information Technology, Shenzhen 518172, China
| | - Xu Deng
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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31
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Nagy SK, Kállai BM, András J, Mészáros T. A novel family of expression vectors with multiple affinity tags for wheat germ cell-free protein expression. BMC Biotechnol 2020; 20:17. [PMID: 32169064 PMCID: PMC7071761 DOI: 10.1186/s12896-020-00610-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background Cell-free protein expression has become a widely used alternative of in vivo, cell-based systems in functional and structural studies of proteins. The wheat germ-based method outstands from the commercially available eukaryotic in vitro translation systems by its flexibility, high translation efficiency and success rate of properly folded eukaryotic protein synthesis. The original T7 promoter containing pEU3-NII vector was improved previously by addition of a ligation-independent cloning site, His6- and GST-tags, and a TEV protease cleavage site to facilitate the creation of recombinant plasmids, permit affinity purification, and enable production of purified, tag-free target proteins, respectively. Results Here, we describe a further development of pEU3-NII vector by inserting the rare-cutting, NotI restriction enzyme cleavage site to simplify vector linearization step prior to in vitro transcription. Additionally, His12, FLAG, and Halo affinity tag coding vectors have been created to increase detection sensitivity, specificity of interaction studies, and provide covalently linkable ligands for pull-down assays, respectively. Finally, the presented GST-His6, and GST-biotin double-tagging vectors could broaden the range of possibilities of protein-protein interaction studies. Conclusions The new generation of pEU3-NII vector family allows a more rapid production of translationally active mRNA and wheat germ cell-free expression of target proteins with a wide variety of affinity tags thus enables designing flexible and diverse experimental arrangement for in vitro studies of proteins.
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Affiliation(s)
- Szilvia Krisztina Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, H-1094, Hungary
| | - Brigitta Margit Kállai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, H-1094, Hungary
| | - Judit András
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, H-1094, Hungary
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, H-1094, Hungary.
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32
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CF-PA 2Vtech: a cell-free human protein array technology for antibody validation against human proteins. Sci Rep 2019; 9:19349. [PMID: 31852950 PMCID: PMC6920144 DOI: 10.1038/s41598-019-55785-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022] Open
Abstract
Antibodies are widely used for the detection of specific molecules such as peptides, proteins, and chemical compounds. The specificity of an antibody is therefore its most important feature. However, it is very difficult to confirm antibody specificity. Recently, we made a human protein array consisting of 19,712 kinds of recombinant human proteins produced by a wheat cell-free protein production system. Here, we demonstrate a novel protein array technology for antibody validation (CF-PA2Vtech). Full-length human cDNAs were fused to N-terminal FLAG-GST and then synthesized by the wheat cell-free system. To construct a 20 K human protein array, about 10 to 14 kinds of human proteins were mixed and captured in each well by glutathione-conjugated magnetic beads in 12 plates or one plate with 384- or 1536-well format, respectively, using a strong magnetic device. Using this protein array plate, commercially available anti-HA or anti-PD-1 antibody reacted to 13 or three human proteins, respectively. The cross-reactivity of these proteins was also confirmed by immunoblotting. These proteins have a similar epitope, and alanine mutations of these epitope candidates dissolved the reactivity. These results indicated that CF-PA2Vtech is very useful for validation of antibodies against human protein.
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33
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Fukuda E, Mori M, Shiku H, Miyahara Y, Kawamura Y, Ogawa K, Ogura T, Goshima N. Development of INSOL-tag for proteome-wide protein handling and its application in protein array analysis. Genes Cells 2019; 25:41-53. [PMID: 31733161 DOI: 10.1111/gtc.12735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 11/30/2022]
Abstract
Proteomic analysis requires protein tags that enable high-throughput handling; however, versatile tags that can be used in in vitro expression systems are currently lacking. In this study, we developed an insoluble protein tag, INSOL-tag, derived from human transcription factor MafG. The INSOL-tagged target protein is expressed in a eukaryotic in vitro expression system and recovered as a pellet following centrifugation at 19,000 × g for 20 min. Comparisons of the target protein recovery rates of GST-tag and INSOL-tag using 111 cytoplasmic proteins revealed a fourfold increase in the yield of INSOL-tagged proteins. Using 267 cancer antigens purified with INSOL-tag, we subsequently developed an INSOL-CTA array method, for profiling autoantibodies in sera of cancer patients. The detection limit of the array was approximately 11.1 pg IgG, and the correlation with ELISA was high (R2 = .993, .955). Moreover, when autoantibody profiling of digestive cancer patient sera was performed, antigen spreading was observed. These data suggest that INSOL-tag is a versatile tag that can insolubilize a wide range of target proteins. It is therefore expected to become a powerful tool in comprehensive protein preparation for protein arrays, antibody production, and mass spectrometry.
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Affiliation(s)
- Eriko Fukuda
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masatoshi Mori
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan
| | - Hiroshi Shiku
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Yoshihiro Miyahara
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | | | - Koji Ogawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan
| | - Toshihiko Ogura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan
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34
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Khambhati K, Bhattacharjee G, Gohil N, Braddick D, Kulkarni V, Singh V. Exploring the Potential of Cell-Free Protein Synthesis for Extending the Abilities of Biological Systems. Front Bioeng Biotechnol 2019; 7:248. [PMID: 31681738 PMCID: PMC6797904 DOI: 10.3389/fbioe.2019.00248] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/16/2019] [Indexed: 12/19/2022] Open
Abstract
Cell-free protein synthesis (CFPS) system is a simple, rapid, and sensitive tool that is devoid of membrane-bound barriers, yet contains all the mandatory substrates, biomolecules, and machineries required for the synthesis of the desired proteins. It has the potential to overcome loopholes in the current in vivo production systems and is a promising tool in both basic and applied scientific research. It facilitates a simplified organization of desired experiments with a variety of reaction conditions, making CFPS a powerful tool in biological research. It has been used for the expansion of genetic code, assembly of viruses, and in metabolic engineering for production of toxic and complex proteins. Subsequently, CFPS systems have emerged as potent technology for high-throughput production of membrane proteins, enzymes, and therapeutics. The present review highlights the recent advances and uses of CFPS systems in biomedical, therapeutic, and biotechnological applications. Additionally, we highlight possible solutions to the potential biosafety issues that may be encountered while using CFPS technology.
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Affiliation(s)
- Khushal Khambhati
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Gargi Bhattacharjee
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Nisarg Gohil
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | | | - Vishwesh Kulkarni
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Vijai Singh
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
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35
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UHRF1-KAT7-mediated regulation of TUSC3 expression via histone methylation/acetylation is critical for the proliferation of colon cancer cells. Oncogene 2019; 39:1018-1030. [PMID: 31582837 DOI: 10.1038/s41388-019-1032-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 01/24/2023]
Abstract
The epigenetic factor UHRF1 regulates transcription by modulating DNA methylation and histone modification, and plays critical roles in proliferation, development, and tumorigenesis. Here, we show that Wnt/c-Myc signaling upregulates UHRF1, which in turn downregulates TUSC3, a candidate tumor suppressor gene that is frequently deleted or downregulated in several cancers. We also show that UHRF1-mediated downregulation of TUSC3 is required for the proliferation of colon cancer cells. Furthermore, we demonstrate that UHRF1 suppresses TUSC3 expression by interacting with methylated H3K14 and thereby suppressing the acetylation of H3K14 by the histone acetyltransferase KAT7. Our study provides evidence for the significance of UHRF1-KAT7-mediated regulation of histone methylation/acetylation in the proliferation of tumor cells and in a diverse set of biological processes controlled by Wnt/c-Myc signaling.
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36
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Miura K, Tachibana M, Takashima E, Morita M, Kanoi BN, Nagaoka H, Baba M, Torii M, Ishino T, Tsuboi T. Malaria transmission-blocking vaccines: wheat germ cell-free technology can accelerate vaccine development. Expert Rev Vaccines 2019; 18:1017-1027. [PMID: 31566026 PMCID: PMC11000147 DOI: 10.1080/14760584.2019.1674145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/25/2019] [Indexed: 12/18/2022]
Abstract
Introduction: Highly effective malaria vaccines are essential component toward malaria elimination. Although the leading malaria vaccine, RTS,S/AS01, with modest efficacy is being evaluated in a pilot feasibility trial, development of a malaria transmission-blocking vaccine (TBV) could make a major contribution toward malaria elimination. Only a few TBV antigens have reached pre-clinical or clinical development but with several challenges including difficulties in the expression of malaria recombinant proteins and low immunogenicity in humans. Therefore, novel approaches to accelerate TBV research to preclinical development are critical to generate an efficacious TBV.Areas covered: PubMed was searched to review the progress and future prospects of malaria TBV research and development. We also reviewed registered trials at ClinicalTrials.gov as well as post-genome TBV candidate discovery research including our efforts.Expert opinion: Wheat germ cell-free protein synthesis technology can accelerate TBV development by overcoming some current challenges of TBV research.
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Affiliation(s)
- Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Mayumi Tachibana
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Masayuki Morita
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Bernard N Kanoi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Minami Baba
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
| | - Motomi Torii
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Tomoko Ishino
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
| | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
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37
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Seto J. On a Robust, Sensitive Cell-Free Method for Pseudomonas Sensing and Quantification in Microfluidic Templated Hydrogels. MICROMACHINES 2019; 10:E506. [PMID: 31370199 PMCID: PMC6723077 DOI: 10.3390/mi10080506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/02/2019] [Accepted: 07/29/2019] [Indexed: 12/19/2022]
Abstract
Through the use of droplet microfluidics to integrate cell-free activity into inert hydrogel beads, we have developed a platform that can perform biologically relevant functions without the need for cells. Specifically, cell-free lysates serve a utility in performing cellular functions and providing biologically relevant metabolic products without requiring the optimal biological conditions for cell growth and proliferation. By teasing out specific biological components that enable transcription and translation to occur, these cell-like functions can be reconstituted in vitro without requiring the entire cell and milieu of cellular organelles. This enables the optimization of synthetic biological circuits, either by concentration or logic switches, simply through the addition or removal of genetic components (plasmids, inducers, or repressors) of regulatory elements. Here, we demonstrate an application of cell-free processes that is robust and portable, independent of a substrate, to apply for sensing and reporting functions of a quorum-sensing molecule N-3-oxododecanoyl homoserine lactone (3OC12HSL) found crucial for pathological Pseudomonas aeruginosa infection. We develop an agarose bead platform that is easily adaptable and simply programmable to fit a variety of biological and chemical sensing applications for the utility of ease of delivery and activation in remote environments-even in conditions with very little hydration.
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Affiliation(s)
- Jong Seto
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco and California, Institute for Quantitative Biosciences (QB3), 1700 4th Street, Byers Hall #303, San Francisco, CA 94158, USA.
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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38
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Sato T, Higashioka K, Sakurai H, Yamamoto T, Goshima N, Ueno M, Sotozono C. Core Transcription Factors Promote Induction of PAX3-Positive Skeletal Muscle Stem Cells. Stem Cell Reports 2019; 13:352-365. [PMID: 31353225 PMCID: PMC6700474 DOI: 10.1016/j.stemcr.2019.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 06/14/2019] [Accepted: 06/25/2019] [Indexed: 12/22/2022] Open
Abstract
The use of adult skeletal muscle stem cells (MuSCs) for cell therapy has been attempted for decades, but still encounters considerable difficulties. MuSCs derived from human induced pluripotent stem cells (hiPSCs) are promising candidates for stem cell therapy to treat Duchenne muscular dystrophy (DMD). Here we report that four transcription factors, HEYL, KLF4, MYOD, and PAX3, selected by comprehensive screening of different MuSC populations, enhance the derivation of PAX3-positive myogenic progenitors from fibroblasts and hiPSCs, using medium that promotes the formation of presomitic mesoderm. These induced PAX3-positive cells contribute efficiently to the repair of DMD-damaged myofibers and also reconstitute the MuSC population. These studies demonstrate how a combination of core transcription factors can fine-tune the derivation of MuSCs capable of contributing to the repair of adult skeletal muscle. Persistent single MyoD can induce myogenic cells, not muscle stem cells The combination of Heyl, Klf4, Pax3, and transient MyoD can induce muscle stem cells Induced PAX3+ cells revealed incorporation into regenerating myofibers of DMD mice
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Affiliation(s)
- Takahiko Sato
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan; Department of Anatomy, Fujita Health University, Toyoake, Aichi, Japan; AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda, Tokyo, Japan.
| | - Koki Higashioka
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan; Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Hidetoshi Sakurai
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan; AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda, Tokyo, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Morio Ueno
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
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39
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Edfors F, Forsström B, Vunk H, Kotol D, Fredolini C, Maddalo G, Svensson AS, Boström T, Tegel H, Nilsson P, Schwenk JM, Uhlen M. Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics. J Proteome Res 2019; 18:2706-2718. [PMID: 31094526 DOI: 10.1021/acs.jproteome.8b00924] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The availability of proteomics resources hosting protein and peptide standards, as well as the data describing their analytical performances, will continue to enhance our current capabilities to develop targeted proteomics methods for quantitative biology. This study describes the analysis of a resource of 26,840 individually purified recombinant protein fragments corresponding to more than 16,000 human protein-coding genes. The resource was screened to identify proteotypic peptides suitable for targeted proteomics efforts, and we report LC-MS/MS assay coordinates for more than 25,000 proteotypic peptides, corresponding to more than 10,000 unique proteins. Additionally, peptide formation and digestion kinetics were, for a subset of the standards, monitored using a time-course protocol involving parallel digestion of isotope-labeled recombinant protein standards and endogenous human plasma proteins. We show that the strategy by adding isotope-labeled recombinant proteins before trypsin digestion enables short digestion protocols (≤60 min) with robust quantitative precision. In a proof-of-concept study, we quantified 23 proteins in human plasma using assay parameters defined in our study and used the standards to describe distinct clusters of individuals linked to different levels of LPA, APOE, SERPINA5, and TFRC. In summary, we describe the use and utility of a resource of recombinant proteins to identify proteotypic peptides useful for targeted proteomics assay development.
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Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Björn Forsström
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Helian Vunk
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - David Kotol
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Claudia Fredolini
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Gianluca Maddalo
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Anne-Sophie Svensson
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Tove Boström
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Atlas Antibodies AB , SE - 114 21 Stockholm , Sweden
| | - Hanna Tegel
- Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Peter Nilsson
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Division of Affinity Proteomics, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, Division of Systems Biology, Department of Protein Science , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Albanova University Center , KTH-Royal Institute of Technology , SE - 171 21 Stockholm , Sweden.,Department of Neuroscience - Karolinska Institute , SE - 171 65 Solna , Sweden.,Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , DK - 2970 Hørsholm , Denmark
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40
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Identification of autoantibodies using human proteome microarrays in patients with IPEX syndrome. Clin Immunol 2019; 203:9-13. [DOI: 10.1016/j.clim.2019.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 03/15/2019] [Accepted: 03/31/2019] [Indexed: 12/15/2022]
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41
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Gregorio NE, Levine MZ, Oza JP. A User's Guide to Cell-Free Protein Synthesis. Methods Protoc 2019; 2:E24. [PMID: 31164605 PMCID: PMC6481089 DOI: 10.3390/mps2010024] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include its open system, the elimination of reliance on living cells, and the ability to focus all system energy on production of the protein of interest. Over the last 60 years, the CFPS platform has grown and diversified greatly, and it continues to evolve today. Both new applications and new types of extracts based on a variety of organisms are current areas of development. However, new users interested in CFPS may find it challenging to implement a cell-free platform in their laboratory due to the technical and functional considerations involved in choosing and executing a platform that best suits their needs. Here we hope to reduce this barrier to implementing CFPS by clarifying the similarities and differences amongst cell-free platforms, highlighting the various applications that have been accomplished in each of them, and detailing the main methodological and instrumental requirement for their preparation. Additionally, this review will help to contextualize the landscape of work that has been done using CFPS and showcase the diversity of applications that it enables.
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Affiliation(s)
- Nicole E Gregorio
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Max Z Levine
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Javin P Oza
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
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42
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Novikova IV, Sharma N, Moser T, Sontag R, Liu Y, Collazo MJ, Cascio D, Shokuhfar T, Hellmann H, Knoblauch M, Evans JE. Protein structural biology using cell-free platform from wheat germ. ADVANCED STRUCTURAL AND CHEMICAL IMAGING 2018; 4:13. [PMID: 30524935 PMCID: PMC6244559 DOI: 10.1186/s40679-018-0062-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022]
Abstract
One of the biggest bottlenecks for structural analysis of proteins remains the creation of high-yield and high-purity samples of the target protein. Cell-free protein synthesis technologies are powerful and customizable platforms for obtaining functional proteins of interest in short timeframes, while avoiding potential toxicity issues and permitting high-throughput screening. These methods have benefited many areas of genomic and proteomics research, therapeutics, vaccine development and protein chip constructions. In this work, we demonstrate a versatile and multiscale eukaryotic wheat germ cell-free protein expression pipeline to generate functional proteins of different sizes from multiple host organism and DNA source origins. We also report on a robust purification procedure, which can produce highly pure (> 98%) proteins with no specialized equipment required and minimal time invested. This pipeline successfully produced and analyzed proteins in all three major geometry formats used for structural biology including single particle analysis with electron microscopy, and both two-dimensional and three-dimensional protein crystallography. The flexibility of the wheat germ system in combination with the multiscale pipeline described here provides a new workflow for rapid production and purification of samples that may not be amenable to other recombinant approaches for structural characterization.
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Affiliation(s)
- Irina V. Novikova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Noopur Sharma
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Trevor Moser
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Ryan Sontag
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Yan Liu
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Michael J. Collazo
- Department of Biological Chemistry, University of California Los Angeles, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095 USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095 USA
| | - Duilio Cascio
- Department of Biological Chemistry, University of California Los Angeles, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095 USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095 USA
| | - Tolou Shokuhfar
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - James E. Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Blvd, Richland, WA 99354 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
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43
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Jaroentomeechai T, Stark JC, Natarajan A, Glasscock CJ, Yates LE, Hsu KJ, Mrksich M, Jewett MC, DeLisa MP. Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery. Nat Commun 2018; 9:2686. [PMID: 30002445 PMCID: PMC6043479 DOI: 10.1038/s41467-018-05110-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/06/2018] [Indexed: 12/13/2022] Open
Abstract
The emerging discipline of bacterial glycoengineering has made it possible to produce designer glycans and glycoconjugates for use as vaccines and therapeutics. Unfortunately, cell-based production of homogeneous glycoproteins remains a significant challenge due to cell viability constraints and the inability to control glycosylation components at precise ratios in vivo. To address these challenges, we describe a novel cell-free glycoprotein synthesis (CFGpS) technology that seamlessly integrates protein biosynthesis with asparagine-linked protein glycosylation. This technology leverages a glyco-optimized Escherichia coli strain to source cell extracts that are selectively enriched with glycosylation components, including oligosaccharyltransferases (OSTs) and lipid-linked oligosaccharides (LLOs). The resulting extracts enable a one-pot reaction scheme for efficient and site-specific glycosylation of target proteins. The CFGpS platform is highly modular, allowing the use of multiple distinct OSTs and structurally diverse LLOs. As such, we anticipate CFGpS will facilitate fundamental understanding in glycoscience and make possible applications in on demand biomanufacturing of glycoproteins. The ability to produce homogeneous glycoproteins is expected to advance fundamental understanding in glycoscience, but current in vivo-based production systems have several limitations. Here, the authors develop an E. coli extract-based one-pot system for customized production of N-linked glycoproteins.
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.,Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL, 60208-3120, USA.,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA
| | - Aravind Natarajan
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Cameron J Glasscock
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Laura E Yates
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Karen J Hsu
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute B224, Evanston, IL, 60208-3120, USA
| | - Milan Mrksich
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.,Department of Cell and Molecular Biology, Northwestern University, Chicago, IL, 60611, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL, 60208-3120, USA. .,Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.
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44
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Xu B, Liu XF, Cai YC, Huang JL, Zhang RX, Chen JH, Cheng XJ, Zhou X, Xu XN, Zhou Y, Zhang T, Chen SB, Li J, Wu QF, Sun CS, Fu YF, Chen JX, Zhou XN, Hu W. Screening for biomarkers reflecting the progression of Babesia microti infection. Parasit Vectors 2018; 11:379. [PMID: 29970143 PMCID: PMC6029176 DOI: 10.1186/s13071-018-2951-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/13/2018] [Indexed: 01/29/2023] Open
Abstract
Background Babesiosis is caused by the invasion of erythrocytes by parasites of the Babesia spp. Babesia microti is one of the primary causative agents of human babesiosis. To better understand the status of the disease, discovering key biomarkers of the different infection stages is crucial. Results This study investigated B. microti infection in the mouse model from 0 to 270 days post-infection (dpi), using blood smears, PCR assays and ELISA. PCR assays showed a higher sensitivity when compared to microscopic examination. Specific IgG antibodies could be detected from 7 days to 270 dpi. Two-dimensional electrophoresis was combined with western blotting and mass spectrometric analysis to screen for specific reactive antigens during both the peak parasitaemia period (7 dpi) and IgG antibody response peak period (30 dpi) by the infected mice plasma. The 87 positive reactive proteins were identified and then expressed with the wheat germ cell-free system. Protein microarrays of all 87 targeted proteins were produced and hybridized with the serial plasma of infected mice model. Based on the antigen reaction profile during the infection procedure, 6 antigens were selected and expressed in Escherichia coli. Due to an early response to IgM, lower immunoreactivity levels of IgG after two months and higher immunoreactivity level IgG during nine months, four recombinant proteins were selected for further characterization, namely rBm2D97(CCF75281.1), rBm2D33(CCF74637.1), rBm2D41(CCF75408.1) and rBm7(CCF73510.1). The diagnostic efficacy of the four recombinant protein candidates was evaluated in a clinical setting using babesiosis patient plasma. The rBm2D33 showed the highest sensitivity with a positive rate of 62.5%. Additional characterization of the two candidate proteins using a mouse vaccination assay, demonstrated that rBm2D41 could reduce peak parasitaemia by 37.4%, indicating its efficacy in preventing severe babesiosis. Conclusions The detection technologies of microscopic examination, PCR assays and antibody tests showed different sensitivities and accuracy during the different stages of B. microti infection. Antibody detection has a unique significance for B. microti infection in the asymptomatic stages. Using immunoreactivity profiles, biomarkers for disease progression were identified and represent useful information for future the diagnosis and vaccine development for this serious disease of public health significance. Electronic supplementary material The online version of this article (10.1186/s13071-018-2951-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Xiu-Feng Liu
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Yu-Chun Cai
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Ji-Lei Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Rui-Xiang Zhang
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Xun-Jia Cheng
- Institute of Biomedical Sciences, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Xia Zhou
- Department of Parasitology, Medical College of Soochow University, Suzhou, People's Republic of China
| | - Xue-Nian Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Yan Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Ting Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Jian Li
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Qun-Feng Wu
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Cheng-Song Sun
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China
| | - Yong-Feng Fu
- Institute of Biomedical Sciences, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Jia-Xu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China
| | - Wei Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Ministry of Science and Technology; Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, Shanghai, People's Republic of China. .,Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, People's Republic of China.
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45
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Engineered membrane protein antigens successfully induce antibodies against extracellular regions of claudin-5. Sci Rep 2018; 8:8383. [PMID: 29849184 PMCID: PMC5976803 DOI: 10.1038/s41598-018-26560-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/15/2018] [Indexed: 01/09/2023] Open
Abstract
The production of antibodies against the extracellular regions (ECR) of multispanning membrane proteins is notoriously difficult because of the low productivity and immunogenicity of membrane proteins due to their complex structure and highly conserved sequences among species. Here, we introduce a new method to generate ECR-binding antibodies utilizing engineered liposomal immunogen prepared using a wheat cell-free protein synthesis system. We used claudin-5 (CLDN-5) as the target antigen, which is a notoriously difficult to produce and poorly immunogenic membrane protein with two highly conserved extracellular loops. We drastically improved the productivity of CLDN-5 in the cell-free system after suppressing and normalizing mRNA GC content. To overcome its low immunogenicity, two engineered antigens were designed and synthesized as proteoliposomes: a human/mouse chimeric CLDN-5, and a CLDN-5-based artificial membrane protein consisting of symmetrically arranged ECRs. Intraperitoneal immunization of both engineered CLDN-5 ECR antigens induced ECR-binding antibodies in mice with a high success rate. We isolated five monoclonal antibodies that specifically recognized CLDN-5 ECR. Antibody clone 2B12 showed high affinity (<10 nM) and inhibited CLDN-5-containing tight junctions. These results demonstrate the effectiveness of the methods for monoclonal antibody development targeting difficult-to-produce membrane proteins such as CLDNs.
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46
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Wang H, Li J, Jewett MC. Development of a Pseudomonas putida cell-free protein synthesis platform for rapid screening of gene regulatory elements. Synth Biol (Oxf) 2018; 3:ysy003. [PMID: 32995512 PMCID: PMC7445763 DOI: 10.1093/synbio/ysy003] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/12/2018] [Accepted: 04/19/2018] [Indexed: 12/21/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems enable the production of protein without the use of living, intact cells. An emerging area of interest is to use CFPS systems to characterize individual elements for genetic programs [e.g. promoters, ribosome binding sites (RBS)]. To enable this research area, robust CFPS systems must be developed from new chassis organisms. One such chassis is the Gram-negative Pseudomonas bacteria, which have been studied extensively for their diverse metabolism with promises in the field of bioremediation and biosynthesis. Here, we report the development and optimization of a high-yielding (198 ± 5.9 µg/ml) batch CFPS system from Pseudomonas putida ATCC 12633. Importantly, both circular and linear DNA templates can be applied directly to the CFPS reaction to program protein synthesis. Therefore, it is possible to prepare hundreds or even thousands of DNA templates without time-consuming cloning work. This opens the possibility to rapidly assess and validate genetic part performance in vitro before performing experiments in cells. To validate the P. putida CFPS system as a platform for prototyping genetic parts, we designed and constructed a library consisting of 15 different RBSs upstream of the reporter protein sfGFP, which covered an order of magnitude range in expression. Looking forward, our P. putida CFPS platform will not only expand the protein synthesis toolkit for synthetic biology but also serve as a platform in expediting the screening and prototyping of gene regulatory elements.
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Affiliation(s)
- He Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.,Master of Biotechnology Program, Northwestern University, Evanston, IL, 60208, USA
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.,Master of Biotechnology Program, Northwestern University, Evanston, IL, 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
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47
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Matsuyama T, Sano N, Takano T, Sakai T, Yasuike M, Fujiwara A, Kawato Y, Kurita J, Yoshida K, Shimada Y, Nakayasu C. Antibody profiling using a recombinant protein–based multiplex ELISA array accelerates recombinant vaccine development: Case study on red sea bream iridovirus as a reverse vaccinology model. Vaccine 2018; 36:2643-2649. [DOI: 10.1016/j.vaccine.2018.03.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/14/2018] [Accepted: 03/22/2018] [Indexed: 01/10/2023]
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48
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Schoborg JA, Jewett MC. Cell-Free Protein Synthesis: An Emerging Technology for Understanding, Harnessing, and Expanding the Capabilities of Biological Systems. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Jennifer A. Schoborg
- Department of Chemical and Biological Engineering; Northwestern University, 2145 Sheridan Road, Evanston, IL; 60208-3120 USA
- Chemistry of Life Processes Institute; 2170 Campus Drive, Evanston, IL; 60208-3120 USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering; Northwestern University, 2145 Sheridan Road, Evanston, IL; 60208-3120 USA
- Chemistry of Life Processes Institute; 2170 Campus Drive, Evanston, IL; 60208-3120 USA
- Robert H. Lurie Comprehensive Cancer Center; Northwestern University, 676 N. St Clair St; Suite 1200 Chicago IL 60611-3068 USA
- Simpson Querrey Institute; Northwestern University; 303 E. Superior St; Suite 11-131, Chicago IL 60611-2875 USA
- Center for Synthetic Biology; Northwestern University, 2145 Sheridan Road; Evanston IL 60208-3120 USA
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49
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Matsumoto M, Nakayama KI. The promise of targeted proteomics for quantitative network biology. Curr Opin Biotechnol 2018; 54:88-97. [PMID: 29550704 DOI: 10.1016/j.copbio.2018.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 02/21/2018] [Accepted: 02/27/2018] [Indexed: 12/20/2022]
Abstract
Proteomics is a powerful tool for obtaining information on a large number of proteins with regard to their expression levels, interactions with other molecules, and posttranslational modifications. Whereas nontargeted, discovery proteomics uncovers differences in the proteomic landscape under different conditions, targeted proteomics has been developed to overcome the limitations of this approach with regard to quantitation. In addition to technical advances in instruments and informatics tools, the advent of the synthetic proteome composed of synthetic peptides or recombinant proteins has advanced the adoption of targeted proteomics across a wide range of research fields. Targeted proteomics can now be applied to measurement of the dynamics of any proteins of interest under a variety of conditions as well as to estimation of the absolute abundance or stoichiometry of proteins in a given network. Multiplexed targeted proteomics assays of high reproducibility and accuracy can provide insight at the quantitative level into entire networks that govern biological phenomena or diseases. Such assays will establish a new paradigm for data-driven science.
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Affiliation(s)
- Masaki Matsumoto
- Department of Molecular and Cellular Biology and Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology and Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
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50
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Damiati S, Kompella UB, Damiati SA, Kodzius R. Microfluidic Devices for Drug Delivery Systems and Drug Screening. Genes (Basel) 2018; 9:E103. [PMID: 29462948 PMCID: PMC5852599 DOI: 10.3390/genes9020103] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/10/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Microfluidic devices present unique advantages for the development of efficient drug carrier particles, cell-free protein synthesis systems, and rapid techniques for direct drug screening. Compared to bulk methods, by efficiently controlling the geometries of the fabricated chip and the flow rates of multiphase fluids, microfluidic technology enables the generation of highly stable, uniform, monodispersed particles with higher encapsulation efficiency. Since the existing preclinical models are inefficient drug screens for predicting clinical outcomes, microfluidic platforms might offer a more rapid and cost-effective alternative. Compared to 2D cell culture systems and in vivo animal models, microfluidic 3D platforms mimic the in vivo cell systems in a simple, inexpensive manner, which allows high throughput and multiplexed drug screening at the cell, organ, and whole-body levels. In this review, the generation of appropriate drug or gene carriers including different particle types using different configurations of microfluidic devices is highlighted. Additionally, this paper discusses the emergence of fabricated microfluidic cell-free protein synthesis systems for potential use at point of care as well as cell-, organ-, and human-on-a-chip models as smart, sensitive, and reproducible platforms, allowing the investigation of the effects of drugs under conditions imitating the biological system.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Uday B Kompella
- Department of Pharmaceutical Sciences, Ophthalmology, and Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Safa A Damiati
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Rimantas Kodzius
- Mathematics and Natural Sciences Department, The American University of Iraq, Sulaimani, Sulaymaniyah 46001, Iraq.
- Materials Genome Institute, Shanghai University, Shanghai 200444, China.
- Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 80539 Munich, Germany.
- Faculty of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany.
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