1
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Koss KM, Son T, Li C, Hao Y, Cao J, Churchward MA, Zhang ZJ, Wertheim JA, Derda R, Todd KG. Toward discovering a novel family of peptides targeting neuroinflammatory states of brain microglia and astrocytes. J Neurochem 2023:10.1111/jnc.15840. [PMID: 37171455 PMCID: PMC10640667 DOI: 10.1111/jnc.15840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Microglia are immune-derived cells critical to the development and healthy function of the brain and spinal cord, yet are implicated in the active pathology of many neuropsychiatric disorders. A range of functional phenotypes associated with the healthy brain or disease states has been suggested from in vivo work and were modeled in vitro as surveying, reactive, and primed sub-types of primary rat microglia and mixed microglia/astrocytes. It was hypothesized that the biomolecular profile of these cells undergoes a phenotypical change as well, and these functional phenotypes were explored for potential novel peptide binders using a custom 7 amino acid-presenting M13 phage library (SX7) to identify unique peptides that bind differentially to these respective cell types. Surveying glia were untreated, reactive were induced with a lipopolysaccharide treatment, recovery was modeled with a potent anti-inflammatory treatment dexamethasone, and priming was determined by subsequently challenging the cells with interferon gamma. Microglial function was profiled by determining the secretion of cytokines and nitric oxide, and expression of inducible nitric oxide synthase. After incubation with the SX7 phage library, populations of SX7-positive microglia and/or astrocytes were collected using fluorescence-activated cell sorting, SX7 phage was amplified in Escherichia coli culture, and phage DNA was sequenced via next-generation sequencing. Binding validation was done with synthesized peptides via in-cell westerns. Fifty-eight unique peptides were discovered, and their potential functions were assessed using a basic local alignment search tool. Peptides potentially originated from proteins ranging in function from a variety of supportive glial roles, including synapse support and pruning, to inflammatory incitement including cytokine and interleukin activation, and potential regulation in neurodegenerative and neuropsychiatric disorders.
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Affiliation(s)
- K M Koss
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Department of Surgery, University of Arizona College of Medicine, Arizona, Tucson, USA
| | - T Son
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
| | - C Li
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
| | - Y Hao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
| | - J Cao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
- 48Hour Discovery Inc, 11421 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada
| | - M A Churchward
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Alberta, Edmonton, Canada
- Department of Biology and Environmental Sciences, Concordia University of Edmonton, Alberta, Edmonton, Canada
| | - Z J Zhang
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
| | - J A Wertheim
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
- Department of Surgery, University of Arizona College of Medicine, Arizona, Tucson, USA
| | - R Derda
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
- 48Hour Discovery Inc, 11421 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada
| | - K G Todd
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Alberta, Edmonton, Canada
- Department of Biomedical Engineering, University of Alberta, Alberta, Edmonton, Canada
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2
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Ramasubramanian A, Muckom R, Sugnaux C, Fuentes C, Ekerdt BL, Clark DS, Healy KE, Schaffer DV. High-Throughput Discovery of Targeted, Minimally Complex Peptide Surfaces for Human Pluripotent Stem Cell Culture. ACS Biomater Sci Eng 2021; 7:1344-1360. [PMID: 33750112 DOI: 10.1021/acsbiomaterials.0c01462] [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] [Indexed: 12/31/2022]
Abstract
Human pluripotent stem cells harbor an unlimited capacity to generate therapeutically relevant cells for applications in regenerative medicine. However, to utilize these cells in the clinic, scalable culture systems that activate defined receptors and signaling pathways to sustain stem cell self-renewal are required; and synthetic materials offer considerable promise to meet these needs. De novo development of materials that target novel pathways has been stymied by a limited understanding of critical receptor interactions maintaining pluripotency. Here, we identify peptide agonists for the human pluripotent stem cell (hPSC) laminin receptor and pluripotency regulator, α6-integrin, through unbiased, library-based panning strategies. Biophysical characterization of adhesion suggests that identified peptides bind hPSCs through α6-integrin with sub-μM dissociation constants similar to laminin. By harnessing a high-throughput microculture platform, we developed predictive guidelines for presenting these integrin-targeting peptides alongside canonical binding motifs at optimal stoichiometries to generate nascent culture surfaces. Finally, when presented as self-assembled monolayers, predicted peptide combinations supported hPSC expansion, highlighting how unbiased screens can accelerate the discovery of targeted biomaterials.
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Affiliation(s)
- Anusuya Ramasubramanian
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Riya Muckom
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Caroline Sugnaux
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Christina Fuentes
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Barbara L Ekerdt
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Kevin E Healy
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States.,Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - David V Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
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3
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Zimmermann JA, Schaffer DV. Engineering biomaterials to control the neural differentiation of stem cells. Brain Res Bull 2019; 150:50-60. [DOI: 10.1016/j.brainresbull.2019.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/09/2019] [Accepted: 05/09/2019] [Indexed: 12/13/2022]
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4
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Sarkes DA, Jahnke JP, Stratis-Cullum DN. Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates. J Vis Exp 2017. [PMID: 29286465 PMCID: PMC5755526 DOI: 10.3791/56061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Biopanning bacterial display libraries is a proven technique for peptide affinity reagent discovery for recognition of both biotic and abiotic targets. Peptide affinity reagents can be used for similar applications to antibodies, including sensing and therapeutics, but are more robust and able to perform in more extreme environments. Specific enrichment of peptide capture agents to a protein target of interest is enhanced using semi-automated sorting methods which improve binding and wash steps and therefore decrease the occurrence of false positive binders. A semi-automated sorting method is described herein for use with a commercial automated magnetic-activated cell sorting device with an unconstrained bacterial display sorting library expressing random 15-mer peptides. With slight modifications, these methods are extendable to other automated devices, other sorting libraries, and other organisms. A primary goal of this work is to provide a comprehensive methodology and expound the thought process applied in analyzing and minimizing the resulting pool of candidates. These techniques include analysis of on-cell binding using fluorescence-activated cell sorting (FACS), to assess affinity and specificity during sorting and in comparing individual candidates, and the analysis of peptide sequences to identify trends and consensus sequences for understanding and potentially improving the affinity to and specificity for the target of interest.
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Affiliation(s)
- Deborah A Sarkes
- Sensors and Electron Devices Directorate, US Army Research Laboratory;
| | - Justin P Jahnke
- Sensors and Electron Devices Directorate, US Army Research Laboratory
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5
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Varun D, Srinivasan GR, Tsai YH, Kim HJ, Cutts J, Petty F, Merkley R, Stephanopoulos N, Dolezalova D, Marsala M, Brafman DA. A robust vitronectin-derived peptide for the scalable long-term expansion and neuronal differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (hNPCs). Acta Biomater 2017; 48:120-130. [PMID: 27989923 DOI: 10.1016/j.actbio.2016.10.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/03/2016] [Accepted: 10/26/2016] [Indexed: 12/22/2022]
Abstract
Despite therapeutic advances, neurodegenerative diseases and disorders remain some of the leading causes of mortality and morbidity in the United States. Therefore, cell-based therapies to replace lost or damaged neurons and supporting cells of the central nervous system (CNS) are of great therapeutic interest. To that end, human pluripotent stem cell (hPSC) derived neural progenitor cells (hNPCs) and their neuronal derivatives could provide the cellular 'raw material' needed for regenerative medicine therapies for a variety of CNS disorders. In addition, hNPCs derived from patient-specific hPSCs could be used to elucidate the underlying mechanisms of neurodegenerative diseases and identify potential drug candidates. However, the scientific and clinical application of hNPCs requires the development of robust, defined, and scalable substrates for their long-term expansion and neuronal differentiation. In this study, we rationally designed a vitronectin-derived peptide (VDP) that served as an adhesive growth substrate for the long-term expansion of several hNPC lines. Moreover, VDP-coated surfaces allowed for the directed neuronal differentiation of hNPC at levels similar to cells differentiated on traditional extracellular matrix protein-based substrates. Overall, the ability of VDP to support the long-term expansion and directed neuronal differentiation of hNPCs will significantly advance the future translational application of these cells in treating injuries, disorders, and diseases of the CNS.
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Sarkes DA, Hurley MM, Stratis-Cullum DN. Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives. Molecules 2016; 21:E1504. [PMID: 27834872 PMCID: PMC6272918 DOI: 10.3390/molecules21111504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022] Open
Abstract
Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC) agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms. Here, we have discovered peptide affinity reagents against abrax, a derivative of abrin with reduced toxicity. Using on-cell Fluorescence Activated Cell Sorting (FACS) assays, we show that the peptides are highly selective for abrax over RiVax, a similar derivative of ricin originally designed as a vaccine, with significant structural homology to abrax. We rank the newly discovered peptides for strongest affinity and analyze three observed consensus sequences with varying affinity and specificity. The strongest (Tier 1) consensus was FWDTWF, which is highly aromatic and hydrophobic. To better understand the observed selectivity, we use the XPairIt peptide-protein docking protocol to analyze binding location predictions of the individual Tier 1 peptides and consensus on abrax and RiVax. The binding location profiles on the two proteins are quite distinct, which we determine is due to differences in pocket size, pocket environment (including hydrophobicity and electronegativity), and steric hindrance. This study provides a model system to show that peptide capture candidates can be quite selective for a structurally similar protein system, even without further maturation, and offers an in silico method of analysis for understanding binding and down-selecting candidates.
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Affiliation(s)
- Deborah A Sarkes
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Margaret M Hurley
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
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7
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Lin E, Sikand A, Wickware J, Hao Y, Derda R. Peptide microarray patterning for controlling and monitoring cell growth. Acta Biomater 2016; 34:53-59. [PMID: 26805426 DOI: 10.1016/j.actbio.2016.01.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 01/09/2016] [Accepted: 01/20/2016] [Indexed: 02/08/2023]
Abstract
The fate of cells is influenced by their microenvironment and many cell types undergo differentiation when stimulated by extracellular cues, such as soluble growth factors and the insoluble extracellular matrix (ECM). Stimulating differentiation by insoluble or "immobilized" cues is a particularly attractive method because it allows for the induction of differentiation in a spatially-defined cohort of cells within a larger subpopulation. To improve the design of de novo screening of such insoluble factors, we describe a methodology for producing high-density peptide microarrays suitable for extended cell culture and fluorescence microscopy. As a model, we used a murine mammary gland cell line (NMuMG) that undergoes epithelial to mesenchymal transition (EMT) in response to soluble transforming growth factor beta (TGF-β) and surface-immobilized peptides that target TGF-β receptors (TGFβRI/II). We repurposed a well-established DNA microarray printing technique to produce arrays of micropatterned surfaces that displayed TGFβRI/II-binding peptides and integrin binding peptides. Upon long-term culture on these arrays, only NMuMG cells residing on EMT-stimulating areas exhibited growth arrest and decreased E-cadherin expression. We believe that the methodology created in this report will aid the development of peptide-decorated surfaces that can locally stimulate defined cell surface receptors and control EMT and other well-characterized differentiation events. STATEMENT OF SIGNIFICANCE Scope of work: This manuscript aims to accelerate the development of instructive biomaterials decorated with specific ligands that target cell-surface receptors and induce specific differentiation of cells upon contact. These materials can be used for practical applications, such as fabricating synthetic materials for large scale, stem cell culture, or investigating differentiation and asymmetric division in stem cells. Specifically, in this manuscript, we repurposed a DNA microarray printer to produce microarrays of peptide-terminated self-assembled monolayers (SAMs). To demonstrate the utility of these arrays in phenotypic assays with mammalian cells, we monitored the induction of epithelial to mesenchymal transition (EMT) in murine mammary epithelial cells using specific peptide ligands printed on these arrays. Novelty: We, and others, have published several strategies for producing peptide-based arrays suitable for long-term phenotypic assays. Many reports relied on patterning steps that made adaptation difficult. The use of a DNA microarray printer as the sole production tool simplified the production of peptide microarrays and increased the throughput of this technology. We confirmed that simplification in production did not compromise the performance of the array; it is still possible to study short-term adhesion, long-term growth, and complex phenotypic responses, such as EMT, in the cells. EMT was studied using immunofluorescent staining after four days of culture. IMPACT This methodology will serve as a foundation for future screening of instructive biomaterials in our research group. As DNA printers are broadly available in academic institutions, we foresee rapid adaptation of this approach by academic researchers.
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8
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Yao S, Liu X, He J, Wang X, Wang Y, Cui FZ. Ordered self-assembled monolayers terminated with different chemical functional groups direct neural stem cell linage behaviours. Biomed Mater 2015; 11:014107. [DOI: 10.1088/1748-6041/11/1/014107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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9
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Integrative Utilization of Microenvironments, Biomaterials and Computational Techniques for Advanced Tissue Engineering. J Biotechnol 2015; 212:71-89. [DOI: 10.1016/j.jbiotec.2015.08.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 08/02/2015] [Accepted: 08/11/2015] [Indexed: 01/13/2023]
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10
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Federico S, Pierce BF, Piluso S, Wischke C, Lendlein A, Neffe AT. Design von Decorin-basierten Peptiden, die an Kollagen I binden, und ihr Potenzial als Adhäsionssequenzen in Biomaterialien. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Federico S, Pierce BF, Piluso S, Wischke C, Lendlein A, Neffe AT. Design of Decorin-Based Peptides That Bind to Collagen I and their Potential as Adhesion Moieties in Biomaterials. Angew Chem Int Ed Engl 2015. [PMID: 26216251 DOI: 10.1002/anie.201505227] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mimicking the binding epitopes of protein-protein interactions by using small peptides is important for generating modular biomimetic systems. A strategy is described for the design of such bioactive peptides without accessible structural data for the targeted interaction, and the effect of incorporating such adhesion peptides in complex biomaterial systems is demonstrated. The highly repetitive structure of decorin was analyzed to identify peptides that are representative of the inner and outer surface, and it was shown that only peptides based on the inner surface of decorin bind to collagen. The peptide with the highest binding affinity for collagen I, LHERHLNNN, served to slow down the diffusion of a conjugated dye in a collagen gel, while its dimer could physically crosslink collagen, thereby enhancing the elastic modulus of the gel by one order of magnitude. These results show the potential of the identified peptides for the design of biomaterials for applications in regenerative medicine.
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Affiliation(s)
- Stefania Federico
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstrasse 55, 14513 Teltow (Germany).,Institute of Chemistry, University of Potsdam, 14476 Potsdam-Golm (Germany)
| | - Benjamin F Pierce
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstrasse 55, 14513 Teltow (Germany)
| | - Susanna Piluso
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstrasse 55, 14513 Teltow (Germany).,Institute of Chemistry, University of Potsdam, 14476 Potsdam-Golm (Germany)
| | - Christian Wischke
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstrasse 55, 14513 Teltow (Germany)
| | - Andreas Lendlein
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstrasse 55, 14513 Teltow (Germany).,Institute of Chemistry, University of Potsdam, 14476 Potsdam-Golm (Germany)
| | - Axel T Neffe
- Institute of Biomaterial Science and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Helmholtz-Zentrum Geesthacht, Kantstrasse 55, 14513 Teltow (Germany). .,Institute of Chemistry, University of Potsdam, 14476 Potsdam-Golm (Germany).
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12
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Rodda AE, Ercole F, Glattauer V, Gardiner J, Nisbet DR, Healy KE, Forsythe JS, Meagher L. Low Fouling Electrospun Scaffolds with Clicked Bioactive Peptides for Specific Cell Attachment. Biomacromolecules 2015; 16:2109-18. [DOI: 10.1021/acs.biomac.5b00483] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Andrew E. Rodda
- Department of Materials Science and Engineering & Monash Institute of Medical Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
- CSIRO Manufacturing
Flagship, Bayview Avenue, Clayton 3168, Victoria, Australia
- Cooperative Research
Centre for Polymers, 8 Redwood Drive, Notting Hill 3168, Victoria, Australia
| | - Francesca Ercole
- Department of Materials Science and Engineering & Monash Institute of Medical Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology,
Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, 381
Royal Parade, Parkville 3052, Victoria, Australia
| | - Veronica Glattauer
- CSIRO Manufacturing
Flagship, Bayview Avenue, Clayton 3168, Victoria, Australia
| | - James Gardiner
- CSIRO Manufacturing
Flagship, Bayview Avenue, Clayton 3168, Victoria, Australia
| | - David R. Nisbet
- School
of Engineering, The Australian National University, Canberra 0200, Australian Capital Territory, Australia
| | - Kevin E. Healy
- Departments
of Bioengineering and Materials Science and Engineering, University of California at Berkeley, Berkeley, California, United States
| | - John S. Forsythe
- Department of Materials Science and Engineering & Monash Institute of Medical Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
| | - Laurence Meagher
- Department of Materials Science and Engineering & Monash Institute of Medical Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
- CSIRO Manufacturing
Flagship, Bayview Avenue, Clayton 3168, Victoria, Australia
- Cooperative Research
Centre for Polymers, 8 Redwood Drive, Notting Hill 3168, Victoria, Australia
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Komura T, Kato K, Konagaya S, Nakaji-Hirabayashi T, Iwata H. Optimization of surface-immobilized extracellular matrices for the proliferation of neural progenitor cells derived from induced pluripotent stem cells. Biotechnol Bioeng 2015; 112:2388-96. [DOI: 10.1002/bit.25636] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 04/17/2015] [Accepted: 04/27/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Takashi Komura
- Institute for Frontier Medical Sciences; Kyoto University; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
| | - Koichi Kato
- Institute for Frontier Medical Sciences; Kyoto University; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
| | - Shuhei Konagaya
- Institute for Frontier Medical Sciences; Kyoto University; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
| | - Tadashi Nakaji-Hirabayashi
- Institute for Frontier Medical Sciences; Kyoto University; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
| | - Hiroo Iwata
- Institute for Frontier Medical Sciences; Kyoto University; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
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14
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Prestwich GD, Healy KE. Why regenerative medicine needs an extracellular matrix. Expert Opin Biol Ther 2014; 15:3-7. [DOI: 10.1517/14712598.2015.975200] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Rodda AE, Meagher L, Nisbet DR, Forsythe JS. Specific control of cell–material interactions: Targeting cell receptors using ligand-functionalized polymer substrates. Prog Polym Sci 2014. [DOI: 10.1016/j.progpolymsci.2013.11.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Affiliation(s)
- Bethany Powell Gray
- Department of Internal Medicine and The Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8807, United States
| | - Kathlynn C. Brown
- Department of Internal Medicine and The Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8807, United States
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Abstract
Over the past three decades, a powerful array of techniques has been developed for expressing heterologous proteins and saccharides on the surface of bacteria. Surface-engineered bacteria, in turn, have proven useful in a variety of settings, including high-throughput screening, biofuel production, and vaccinology. In this chapter, we provide a comprehensive review of methods for displaying polypeptides and sugars on the bacterial cell surface, and discuss the many innovative applications these methods have found to date. While already an important biotechnological tool, we believe bacterial surface display may be further improved through integration with emerging methodology in other fields, such as protein engineering and synthetic chemistry. Ultimately, we envision bacterial display becoming a multidisciplinary platform with the potential to transform basic and applied research in bacteriology, biotechnology, and biomedicine.
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18
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Ekerdt BL, Segalman RA, Schaffer DV. Spatial organization of cell-adhesive ligands for advanced cell culture. Biotechnol J 2013; 8:1411-23. [PMID: 24318636 PMCID: PMC4282480 DOI: 10.1002/biot.201300302] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/10/2013] [Accepted: 09/26/2013] [Indexed: 01/31/2023]
Abstract
Interaction between biomaterials and cells is a critical aspect for successful application of tissue engineering research. Technological advances within the past decade have enabled a number of studies to investigate how the spatial organization of cell-adhesive ligands impacts complex and rich cell behaviors ranging from adhesion to differentiation. Cells in their native environment are surrounded by chemical and physical factors spanning a range of length scales from nanometers to hundreds of microns. Furthermore, signals in the form of cell-adhesive ligands presented from this environment in different size scales and/or geometrical arrangements can change how a cell senses and responds to its surroundings. Biology can thus convey information not only in the concentration of a ligand but through its ability to change the spatial organization of these cues, raising questions both on the mechanisms by which it patterns such information and on the means by which a cell interprets it. This review discusses major findings associated with various systems developed to study cell-adhesive ligand presentation as well as an overview of the important material systems used in these studies. Promising material systems to further investigations in this field are also examined. Future directions will likely include determining how cells sense local and global ligand concentrations, understanding underlying mechanisms that regulate cell behaviors, and investigating the function of more complex cell types and diverse ligands.
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Affiliation(s)
- Barbara L Ekerdt
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
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19
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Bonham AJ, Paden NG, Ricci F, Plaxco KW. Detection of IP-10 protein marker in undiluted blood serum via an electrochemical E-DNA scaffold sensor. Analyst 2013; 138:5580-3. [PMID: 23905162 PMCID: PMC3956051 DOI: 10.1039/c3an01079a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe an electrochemical analog of fluorescence polarization that supports the quantitative measurement of a specific protein, the chemokine IP-10, directly in undiluted blood serum. The sensor is label-free, wash-free, and electronic, suggesting it could support point-of-care detection of diagnostic proteins in largely unprocessed clinical samples.
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Affiliation(s)
- Andrew J. Bonham
- Department of Chemistry, Metropolitan State University of Denver, Denver, CO 80217, USA. Fax: 01 303 556 5399; Tel: 01 303 556 3929;
| | - Nicole G. Paden
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93117, USA. Fax: 01 805 893 4120; Tel: 01 805 893 5558;
| | - Francesco Ricci
- University of Rome Tor Vergata, Rome, Italy. Tel: 39 06 72594422;
| | - Kevin W. Plaxco
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93117, USA. Fax: 01 805 893 4120; Tel: 01 805 893 5558;
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20
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Polymersomes-mediated delivery of fluorescent probes for targeted and long-term imaging in live cell microscopy. Methods Mol Biol 2013; 991:343-51. [PMID: 23546683 DOI: 10.1007/978-1-62703-336-7_31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Fluorescent microscopy becomes an essential tool for live imaging analysis of complex biological pathways and events as it enables noninvasive real-time/real-space imaging. The design of fluorescent probes to provide dynamic information and long-term tracking of samples without altering physiological and structural integrity is critical in live imaging. In recent years, nanotechnology has produced a new generation of imaging probes with promising applications in live imaging. In particular, we describe the use of pH-sensitive amphiphilic block copolymer PMPC25-PDPA70. This polymer forms biomimetic nanometer-sized vesicles (known as polymersomes) that are readily uptaken by a wide variety of cell types. The pH sensitivity confers much needed endolysomal escape capability without inducing cellular toxicity or stress. Two different characteristic compartments in the polymersomes (hydrophilic core and hydrophobic membrane) allow for encapsulation of different labeling cargoes such as lipidic cell membrane probes, quantum dots, fluorescent dyes, and fluorescent biomolecules such as nucleic acid and protein probes.
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Abstract
Within the adult organism, stem cells reside in defined anatomical microenvironments called niches. These architecturally diverse microenvironments serve to balance stem cell self-renewal and differentiation. Proper regulation of this balance is instrumental to tissue repair and homeostasis, and any imbalance can potentially lead to diseases such as cancer. Within each of these microenvironments, a myriad of chemical and physical stimuli interact in a complex (synergistic or antagonistic) manner to tightly regulate stem cell fate. The in vitro replication of these in vivo microenvironments will be necessary for the application of stem cells for disease modeling, drug discovery, and regenerative medicine purposes. However, traditional reductionist approaches have only led to the generation of cell culture methods that poorly recapitulate the in vivo microenvironment. To that end, novel engineering and systems biology approaches have allowed for the investigation of the biological and mechanical stimuli that govern stem cell fate. In this review, the application of these technologies for the dissection of stem cell microenvironments will be analyzed. Moreover, the use of these engineering approaches to construct in vitro stem cell microenvironments that precisely control stem cell fate and function will be reviewed. Finally, the emerging trend of using high-throughput, combinatorial methods for the stepwise engineering of stem cell microenvironments will be explored.
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Affiliation(s)
- David A Brafman
- Department of Cellular and Molecular Medicine, Stem Cell Program, University of California at San Diego, La Jolla, California
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22
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Enhanced proliferation and differentiation of neural stem cells grown on PHA films coated with recombinant fusion proteins. Acta Biomater 2013; 9:7845-54. [PMID: 23639778 DOI: 10.1016/j.actbio.2013.04.038] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/20/2013] [Accepted: 04/16/2013] [Indexed: 12/20/2022]
Abstract
Polyhydroxyalkanoates (PHAs) belong to a family of copolyesters with demonstrated biocompatibility. We hypothesize that genetically fusing evolutionarily preserved cell binding motifs, such as RGD or IKVAV, to the PHA-binding protein phasin (PhaP) for surface functionalization of PHA materials could better support the growth and differentiation of neural stem cells (NSCs). This hypothesis is tested on three polyester materials of the same aliphatic family: poly(L-lactic acid) (PLA) and two PHB copolymers, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-3-hydroxyhexanoate) (PHBVHHx). Experimental results indicate that surface coating of the two fusion proteins, PhaP-RGD and PhaP-IKVAV, provides short-term advantages in promoting the adhesion, proliferation and neural differentiation of rat NSCs compared to the PhaP-coated or uncoated material. Among the tested samples, the combination of coating PhaP-IKVAV on an PHBVHHx surface yields the highest levels in cell adhesion and proliferation, while the PLA film coated with PhaP-IKVAV promotes better neural differentiation and neurite outgrowth in the early stage. Because both PhaP-RGD and PhaP-IKVAV could be produced in an inexpensive manner, our data suggest that PhaP-IKVAV is an ideal nonspecific coating agent to functionalize hydrophobic biomaterials in the application of neural tissue engineering.
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23
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Caprini A, Silva D, Zanoni I, Cunha C, Volontè C, Vescovi A, Gelain F. A novel bioactive peptide: assessing its activity over murine neural stem cells and its potential for neural tissue engineering. N Biotechnol 2013; 30:552-62. [PMID: 23541699 DOI: 10.1016/j.nbt.2013.03.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 02/11/2013] [Accepted: 03/18/2013] [Indexed: 01/16/2023]
Abstract
The design of biomimetic scaffolds suitable for cell-based therapies is a fundamental step for the regeneration of the damaged nervous system; indeed growing interest is focusing on the discovery of peptide sequences to modulate the fate of transplanted cells and, in particular, the differentiation outcome of multipotent neural stem cells. By applying the Phage Display technique to murine neural stem cells we isolated a peptide, KLPGWSG, present in proteins involved in both stem cell maintenance and differentiation. We show that KLPGWSG binds molecules expressed on the cell surface of murine adult neural stem cells, thus may potentially be involved in stem cell fate determination. Indeed we demonstrated that this peptide in solution enhances per se cell differentiation toward the neuronal phenotype. Hence, we synthesized two LDLK-12-based self-assembling peptides functionalized with KLPGWSG peptide (KLP and Ac-KLP) and characterized them via atomic force microscopy, rheometry and circular dichroism, obtaining nanostructured hydrogels supporting murine neural stem cells differentiation in vitro. Interestingly, we demonstrated that, when scaffold stiffness is comparable to that of the brain in vivo, the Ac-KLP SAP-based scaffold enhances the neuronal differentiation of neural stem cells. These evidences place both KLPGWSG and the functionalized self-assembling peptide Ac-KLP as promising candidates for, respectively, biomimetic studies and stem cell therapies for nervous regeneration.
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Affiliation(s)
- Andrea Caprini
- Center for Nanomedicine and Tissue Engineering, A.O. Ospedale Niguarda Ca' Granda, Milan 20162, Italy
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24
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Mei Y. Microarrayed Materials for Stem Cells. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2012; 15:10.1016/S1369-7021(12)70196-7. [PMID: 24311967 PMCID: PMC3848960 DOI: 10.1016/s1369-7021(12)70196-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Stem cells hold remarkable promise for applications in disease modeling, cancer therapy and regenerative medicine. Despite the significant progress made during the last decade, designing materials to control stem cell fate remains challenging. As an alternative, materials microarray technology has received great attention because it allows for high throughput materials synthesis and screening at a reasonable cost. Here, we discuss recent developments in materials microarray technology and their applications in stem cell engineering. Future opportunities in the field will also be reviewed.
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Affiliation(s)
- Ying Mei
- Clemson-MUSC Bioengineering Program, Department of Bioengineering, Clemson University, Charleston, SC 29425, USA
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25
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Abstract
Biointegration refers to the interconnection between a biomedical device and the recipient tissue. In many implant devices, the lack of proper biointegration can cause device failure and potentially serious medical problems. This review summarizes the recent progress in surface chemistry, drug delivery and antifouling methods to improve the biointegration of implants. Much progress has been made as our understanding of biological systems and material properties expands and as new technologies become available. This article addresses methods of enhancing biointegration by means of modifying implant surface chemistry and by drug-delivery approaches.
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Higuchi A, Ling QD, Hsu ST, Umezawa A. Biomimetic cell culture proteins as extracellular matrices for stem cell differentiation. Chem Rev 2012; 112:4507-40. [PMID: 22621236 DOI: 10.1021/cr3000169] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Akon Higuchi
- Department of Chemical and Materials Engineering, National Central University, Jhongli, Taoyuan, 32001 Taiwan.
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27
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Abstract
Peptides are increasingly used as therapeutic and diagnostic agents. The combination of bacterial cell-surface display peptide libraries with magnetic- and fluorescence-activated cell sorting technologies provides an efficient and highly effective methodology to identify and engineer peptides for a growing number of molecular recognition applications. Here, detailed protocols for both the generation and screening of bacterial display peptide libraries are presented. The methods described enable the discovery and evolutionary optimization of protein-binding peptides, cell-specific peptides, and enzyme substrates for diverse biotechnology applications.
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Affiliation(s)
- Jennifer A Getz
- Department of Chemical Engineering, Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California, USA
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28
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Kogot JM, Zhang Y, Moore SJ, Pagano P, Stratis-Cullum DN, Chang-Yen D, Turewicz M, Pellegrino PM, de Fusco A, Soh HT, Stagliano NE. Screening of peptide libraries against protective antigen of Bacillus anthracis in a disposable microfluidic cartridge. PLoS One 2011; 6:e26925. [PMID: 22140433 PMCID: PMC3225367 DOI: 10.1371/journal.pone.0026925] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/05/2011] [Indexed: 11/21/2022] Open
Abstract
Bacterial surface peptide display has gained popularity as a method of affinity reagent generation for a wide variety of applications ranging from drug discovery to pathogen detection. In order to isolate the bacterial clones that express peptides with high affinities to the target molecule, multiple rounds of manual magnetic activated cell sorting (MACS) followed by multiple rounds of fluorescence activated cell sorting (FACS) are conventionally used. Although such manual methods are effective, alternative means of library screening which improve the reproducibility, reduce the cost, reduce cross contamination, and minimize exposure to hazardous target materials are highly desired for practical application. Toward this end, we report the first semi-automated system demonstrating the potential for screening bacterially displayed peptides using disposable microfluidic cartridges. The Micro-Magnetic Separation platform (MMS) is capable of screening a bacterial library containing 3 × 10¹⁰ members in 15 minutes and requires minimal operator training. Using this system, we report the isolation of twenty-four distinct peptide ligands that bind to the protective antigen (PA) of Bacilus anthracis in three rounds of selection. A consensus motif WXCFTC was found using the MMS and was also found in one of the PA binders isolated by the conventional MACS/FACS approach. We compared MMS and MACS rare cell recovery over cell populations ranging from 0.1% to 0.0000001% and found that both magnetic sorting methods could recover cells down to 0.0000001% initial cell population, with the MMS having overall lower standard deviation of cell recovery. We believe the MMS system offers a compelling approach towards highly efficient, semi-automated screening of molecular libraries that is at least equal to manual magnetic sorting methods and produced, for the first time, 15-mer peptide binders to PA protein that exhibit better affinity and specificity than peptides isolated using conventional MACS/FACS.
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Affiliation(s)
- Joshua M. Kogot
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - Yanting Zhang
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Stephen J. Moore
- CytomX Therapeutics, LLC, Santa Barbara, California, United States of America
| | - Paul Pagano
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Dimitra N. Stratis-Cullum
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - David Chang-Yen
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Marek Turewicz
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - Paul M. Pellegrino
- United States Army Research Laboratory, Sensors and Electron Devices Directorate, Adelphi, Maryland, United States of America
| | - Andre de Fusco
- Cynvenio Biosystems, Inc., Westlake Village, California, United States of America
| | - H. Tom Soh
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Nancy E. Stagliano
- CytomX Therapeutics, LLC, Santa Barbara, California, United States of America
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29
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30
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Löfblom J. Bacterial display in combinatorial protein engineering. Biotechnol J 2011; 6:1115-29. [DOI: 10.1002/biot.201100129] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/15/2011] [Accepted: 06/20/2011] [Indexed: 12/17/2022]
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31
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Derda R, Tang SKY, Li SC, Ng S, Matochko W, Jafari MR. Diversity of phage-displayed libraries of peptides during panning and amplification. Molecules 2011; 16:1776-803. [PMID: 21339712 PMCID: PMC6259649 DOI: 10.3390/molecules16021776] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 02/10/2011] [Accepted: 02/17/2011] [Indexed: 01/15/2023] Open
Abstract
The amplification of phage-displayed libraries is an essential step in the selection of ligands from these libraries. The amplification of libraries, however, decreases their diversity and limits the number of binding clones that a screen can identify. While this decrease might not be a problem for screens against targets with a single binding site (e.g., proteins), it can severely hinder the identification of useful ligands for targets with multiple binding sites (e.g., cells). This review aims to characterize the loss in the diversity of libraries during amplification. Analysis of the peptide sequences obtained in several hundred screens of peptide libraries shows explicitly that there is a significant decrease in library diversity that occurs during the amplification of phage in bacteria. This loss during amplification is not unique to specific libraries: it is observed in many of the phage display systems we have surveyed. The loss in library diversity originates from competition among phage clones in a common pool of bacteria. Based on growth data from the literature and models of phage growth, we show that this competition originates from growth rate differences of only a few percent for different phage clones. We summarize the findings using a simple two-dimensional "phage phase diagram", which describes how the collapse of libraries, due to panning and amplification, leads to the identification of only a subset of the available ligands. This review also highlights techniques that allow elimination of amplification-induced losses of diversity, and how these techniques can be used to improve phage-display selection and enable the identification of novel ligands.
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Affiliation(s)
- Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G2G2, Canada.
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