Name: screening and identification of small peptides targeting fibroblast growth factor receptor2 using a phage display peptide library
Uploaded: 2019-09-30T15:00:00
Description: Watch this Scientific Journal Video about Screening and Identification of Small Peptides Targeting Fibroblast Growth Factor Receptor2 using a Phage Display Peptide Library at JoVE.com

This work was supported by the Science and Technology Program of Guangzhou (No. 2016201604030039).

1. Reagent preparation
<ol>
	<li>LB (lysogeny broth) medium: Dissolve 1 g of tryptone, 0.5 g of yeast extract, and 0.5 g of NaCl in 100 mL of H2O. Autoclave and store at 4 &#176;C.</li>
	<li>Tetracycline stock: Prepare 20 mg/mL in 1:1 ethanol:H2O. Store at -20 &#176;C, and vortex before using.</li>
	<li>IPTG/X-gal solution: Mix 0.5 g of IPTG (isopropyl &#946;-D-1-thiogalactopyranoside) and 0.4 g of X-gal (5-bromo-4-chloro-3-indolyl &#946;-D-galactoside) in 10 mL of DMF (dimethyl formamide). The so...

<ol>
	<li>Eswarakumar, V. P., Lax, I., Schlessinger, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+signaling+by+fibroblast+growth+factor+receptors.">Cellular signaling by fibroblast growth factor receptors.</a> Cytokine &amp; Growth Factor Reviews. 16 (2), 139-149 (2005).</li><li>Turner, N., Grose, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fibroblast+growth+factor+signaling:+from+development+to+cancer.">Fibroblast growth factor signaling: from development to cancer.</a> Nature Reviews Cancer. 10 (2), 116-129 (2010).</li><li>Cancer Genome Atlas Network. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+molecular+portraits+of+human+breast+tumors.">Comprehensive molecular portraits of human breast tumors.</a> Nature. 490 (7418), 61-70 (2012).</li><li>Matsumoto, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FGFR2+gene+amplification+and+clinicopathological+features+in+gastric+cancer.">FGFR2 gene amplification and clinicopathological features in gastric cancer.</a> British Journal of Cancer. 106 (4), 727-732 (2012).</li><li>Weiss, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frequent+and+focal+FGFR1+amplification+associates+with+therapeutically+tractable+FGFR1+dependency+in+squamous+cell+lung+cancer.">Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer.</a> Science Translational Medicine. 2 (62), 62ra93 (2010).</li><li>Babina, I. S., Turner, N. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+and+challenges+in+targeting+FGFR+signaling+in+cancer.">Advances and challenges in targeting FGFR signaling in cancer.</a> Nature Reviews Cancer. 17 (5), 318-322 (2017).</li><li>Katoh, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fibroblast+growth+factor+receptors+as+treatment+targets+in+clinical+oncology.">Fibroblast growth factor receptors as treatment targets in clinical oncology.</a> Nature Reviews Clinical Oncology. 16 (2), 105-122 (2019).</li><li>Soria, J. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phase+I/IIa+study+evaluating+the+safety,+efficacy,+pharmacokinetics,+and+pharmacodynamics+of+lucitanib+in+advanced+solid+tumors.">Phase I/IIa study evaluating the safety, efficacy, pharmacokinetics, and pharmacodynamics of lucitanib in advanced solid tumors.</a> Annals of Oncology. 25 (11), 2244-2251 (2014).</li><li>French, D. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+FGFR4+inhibits+hepatocellular+carcinoma+in+preclinical+mouse+models.">Targeting FGFR4 inhibits hepatocellular carcinoma in preclinical mouse models.</a> PLoS ONE. 7 (5), e36713 (2012).</li><li>Martinez-Torrecuadrada, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+the+extracellular+domain+of+fibroblast+growth+factor+receptor+3+with+human+single-chain+Fv+antibodies+inhibits+bladder+carcinoma+cell+line+proliferation.">Targeting the extracellular domain of fibroblast growth factor receptor 3 with human single-chain Fv antibodies inhibits bladder carcinoma cell line proliferation.</a> Clinical Cancer Research. 11 (17), 6280-6290 (2005).</li><li>Palamakumbura, A. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lysyl+oxidase+propeptide+inhibits+prostate+cancer+cell+growth+by+mechanisms+that+target+FGF-2-cell+binding+and+signaling.">Lysyl oxidase propeptide inhibits prostate cancer cell growth by mechanisms that target FGF-2-cell binding and signaling.</a> Oncogene. 28 (38), 3390-3400 (2009).</li><li>Ladner, R. C., Sato, A. K., Gorzelany, J., de Souza, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phage+display-derived+peptides+as+therapeutic+alternatives+to+antibodies.">Phage display-derived peptides as therapeutic alternatives to antibodies.</a> Drug Discovery Today. 9 (12), 525-529 (2004).</li><li>Wu, C. H., Liu, I. J., Lu, R. M., Wu, H. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advancement+and+applications+of+peptide+phage+display+technology+in+biomedical+science.">Advancement and applications of peptide phage display technology in biomedical science.</a> Journal of Biomedical Science. 23, 8 (2016).</li><li>Kay, B. K., Kasanov, J., Yamabhai, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Screening+phage-displayed+combinatorial+peptide+libraries.">Screening phage-displayed combinatorial peptide libraries.</a> Methods. 24 (3), 240-246 (2001).</li><li>Rodi, D. J., Makowski, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phage-display+technology+-+Finding+a+needle+in+a+vast+molecular+haystack.">Phage-display technology - Finding a needle in a vast molecular haystack.</a> Current Opinion in Biotechnology. 10, 87-93 (1999).</li><li>Sidhu, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineering+M13+for+phage+display.">Engineering M13 for phage display.</a> Biomolecular Engineering. 18, 57-63 (2002).</li><li>Hamzeh-Mivehroud, M., Mahmoudpour, A., Dastmalchi, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+new+peptide+ligands+for+epidermal+growth+factor+receptor+using+phage+display+and+computationally+modeling+their+mode+of+binding.">Identification of new peptide ligands for epidermal growth factor receptor using phage display and computationally modeling their mode of binding.</a> Chemical Biology &amp; Drug Design. 79 (3), 246-259 (2012).</li><li>Askoxylakis, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Peptide-based+targeting+of+the+platelet-derived+growth+factor+receptor+beta.">Peptide-based targeting of the platelet-derived growth factor receptor beta.</a> Molecular Imaging and Biology. 15 (2), 212-221 (2013).</li><li>Chen, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transdermal+protein+delivery+by+a+coadministered+peptide+identified+via+phage+display.">Transdermal protein delivery by a coadministered peptide identified via phage display.</a> Nature Biotechnology. 24 (4), 455-460 (2006).</li><li>Azzazy, H. M., Highsmith, W. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phage+display+technology:+clinical+applications+and+recent+innovations.">Phage display technology: clinical applications and recent innovations.</a> Clinical Biochemistry. 35, 425-445 (2002).</li><li>Pasqualini, R., Ruoslahti, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organ+targeting+In+vivo+using+phage+display+peptide+libraries.">Organ targeting In vivo using phage display peptide libraries.</a> Nature. 380 (6572), 364-366 (1996).</li><li>Liu, R., Li, X., Xiao, W., Lam, K. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tumor-targeting+peptides+from+combinatorial+libraries.">Tumor-targeting peptides from combinatorial libraries.</a> Advanced Drug Delivery Reviews. 110-111, 13-37 (2017).</li><li>Binetruy-Tournaire, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+a+peptide+blocking+vascular+endothelial+growth+factor+(VEGF)-mediated+angiogenesis.">Identification of a peptide blocking vascular endothelial growth factor (VEGF)-mediated angiogenesis.</a> The EMBO Journal. 19, 1525-1533 (2000).</li><li>Peng, Y., Zhang, Y., Mitchell, W. J., Zhang, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+a+Lipopolysaccharide-Targeted+Peptide+Mimic+Vaccine+against+Q+Fever.">Development of a Lipopolysaccharide-Targeted Peptide Mimic Vaccine against Q Fever.</a> Journal of Immunology. 189, 4909-4920 (2012).</li><li>Lamichhane, T. N., Abeydeera, N. D., Duc, A. C., Cunningham, P. R., Chow, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selection+of+Peptides+Targeting+Helix+31+of+Bacterial+16S+Ribosomal+RNA+by+Screening+M13+Phage-Display+Libraries.">Selection of Peptides Targeting Helix 31 of Bacterial 16S Ribosomal RNA by Screening M13 Phage-Display Libraries.</a> Molecules. 16, 1211-1239 (2011).</li><li>Sahin, D., Taflan, S. O., Yartas, G., Ashktorab, H., Smoot, D. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Screening+and+Identification+of+Peptides+Specifically+Targeted+to+Gastric+Cancer+Cells+from+a+Phage+Display+Peptide+Library.+Asian+Pacific.">Screening and Identification of Peptides Specifically Targeted to Gastric Cancer Cells from a Phage Display Peptide Library. Asian Pacific.</a> Journal of Cancer Prevention. 19 (4), 927-932 (2018).</li><li>Kelly, K. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeted+nanoparticles+for+imaging+incipient+pancreatic+ductal+adenocarcinoma.">Targeted nanoparticles for imaging incipient pancreatic ductal adenocarcinoma.</a> PLOS Medicine. 5 (4), e85 (2008).</li><li>Sugihara, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+pro-apoptotic+peptides+as+potential+therapy+for+peritoneal+endometriosis.">Development of pro-apoptotic peptides as potential therapy for peritoneal endometriosis.</a> Nature Communications. 5, 4478 (2014).</li><li>Rafii, S., Avecilla, S. T., Jin, D. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tumor+vasculature+address+book:+Identification+of+stage-specific+tumor+vessel+zip+codes+by+phage+display.">Tumor vasculature address book: Identification of stage-specific tumor vessel zip codes by phage display.</a> Cancer Cell. 4, 331-333 (2003).</li><li>Arap, W., Pasqualini, R., Ruoslahti, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cancer+Treatment+by+Targeted+Drug+Delivery+to+Tumor+Vasculature+in+a+Mouse+Model.">Cancer Treatment by Targeted Drug Delivery to Tumor Vasculature in a Mouse Model.</a> Science. 279, 377-390 (1997).</li></ol>

A combinatorial phage library is a powerful and effective tool for high-throughput screening of novel peptides that can bind target molecules and regulate their function13. Currently, phage display peptide libraries have a wide range of applications. For example, they can be used for selecting bioactive peptides bound to receptor proteins23, non-protein targets24,25, disease-specific antigen mimics...

Fibroblast growth factor receptors (FGFRs) play key roles in cell proliferation, wound healing, and angiogenesis in vivo1. Aberrant activation of FGFR signaling observed in a variety of tumors2,3,4,5 includes gene amplification, gene mutations, chromosomal aberrations, and excessive ligand secretion6. Many inhibitors targeting FGFRs have shown promising therapeutic effects in clinical trials and are mainly classified into three types: (1) small molecule kinase inhibitors, which bind to the intracellular domain of FGFR, (2) antagonists targeting the extracellular segment, and (3) FGF ligand traps6. Although several of the small molecule kinase inhibitors have good therapeutic effects both in vitro and in vivo7, most of them have poor target specificity and show adverse effects such as hypertension8. The majority of the antagonists are monoclonal antibodies9,10 and polypeptides11. Peptides have advantages over small molecules due to their specificity and lower side effects. They also retain cell permeability and do not accumulate in specific organs as compared to protein drugs12. Hence, targeted small peptides are both effective and prospective therapeutic agents.
Phage display technology is an easy but powerful tool for identifying small peptides which can bind to a given molecule13,14,15. We used a phage display peptide library that is based on a simple M13 phage with over 109 different peptide sequences displayed at the tail for binding to the target molecule (see Table of Materials)16. Due to the high affinity of phages towards the given molecule, unbound phages can be washed away, and only tightly bound phages with the desired short peptides are retained. The given molecular targets can be immobilized proteins17,18, carbohydrates, cultured cells, or even inorganic materials19,20. An exciting case was reported where organ-specific peptides were selected in vivo using phage display technology21. The advantages of phage display technology include high throughput, ease of operation, low cost and a wide range of applications22.
In this study, we provide a detailed protocol of screening small peptides binding to the immobilized protein (FGFR2) using a phage display library. The efficacy of the technology is also examined by measuring the affinity of the obtained peptide towards FGFR2 by Isothermal Titration Calorimetry (ITC), and the biological activity by a cell proliferation assay. The method may be extended for screening small peptides that bind to carbohydrates, cultured cells, or even inorganic materials.

<table>
	<tbody>
		<tr>
			<td>0.22 &#956;m Filter</td>
			<td>Merck Millipore</td>
			<td>MPGP002A1</td>
			<td></td>
		</tr>
		<tr>
			<td>35 cm2 Small dish</td>
			<td>Thermo</td>
			<td>150460</td>
			<td></td>
		</tr>
		<tr>
			<td>70% Ethanol</td>
			<td>Guangzhou chemical reagent factory</td>
			<td>64-17-5</td>
			<td></td>
		</tr>
		<tr>
			<td>-96 gIII sequencing primer</td>
			<td></td>
			<td></td>
			<td>Synthesis from Sangon Biotech (Shanghai) Co., Ltd.</td>
		</tr>
		<tr>
			<td>96-well plate</td>
			<td>Nest</td>
			<td>701001-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Beyotime</td>
			<td>ST004D</td>
			<td></td>
		</tr>
		<tr>
			<td>Bacto-Tryptone</td>
			<td>Oxoid</td>
			<td>L0037</td>
			<td></td>
		</tr>
		<tr>
			<td>BALB/c 3T3 cells</td>
			<td>ATCC</td>
			<td>CRL-&#173;6587</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Biodragon</td>
			<td>BD-M10110</td>
			<td></td>
		</tr>
		<tr>
			<td>CCK-8 kit</td>
			<td>DOJINDO</td>
			<td>CK04</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Hyclone</td>
			<td>sh30243.01</td>
			<td></td>
		</tr>
		<tr>
			<td>DMF</td>
			<td>Newprobe</td>
			<td>PB10247</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Invitrogen</td>
			<td>15576028</td>
			<td></td>
		</tr>
		<tr>
			<td>FGF2 Protein</td>
			<td>Sino Biological Inc.</td>
			<td>10014-HNAE</td>
			<td>Purity &#62;95%</td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma</td>
			<td>G8898-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>IPTG</td>
			<td>Beyotime</td>
			<td>ST097</td>
			<td></td>
		</tr>
		<tr>
			<td>ITC200 system</td>
			<td>MicroCal Omega</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma</td>
			<td>S6191</td>
			<td></td>
		</tr>
		<tr>
			<td>NaHCO3</td>
			<td>Guangzhou chemical reagent factory</td>
			<td>144-55-8</td>
			<td></td>
		</tr>
		<tr>
			<td>NaI</td>
			<td>Bidepharm</td>
			<td>BD40879</td>
			<td></td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td>Guangzhou chemical reagent factory</td>
			<td>1310-73-2</td>
			<td></td>
		</tr>
		<tr>
			<td>PEG&#8211;8000</td>
			<td>Sigma</td>
			<td>P2139-250</td>
			<td></td>
		</tr>
		<tr>
			<td>Ph.D.-7 phage display peptide library kit</td>
			<td>New England BioLabs</td>
			<td>E8100S</td>
			<td>Containing the Ph.D.-7 phage library, E. coli ER2738 host strain and M13KE control phage</td>
		</tr>
		<tr>
			<td>Recombinant FGFR2 extracellular domain proteins</td>
			<td>Sino Biological Inc.</td>
			<td>10824-H08H</td>
			<td>Purity &#62; 97%</td>
		</tr>
		<tr>
			<td>Small peptide</td>
			<td></td>
			<td></td>
			<td>Synthesis from GL Biochem Ltd. (Shanghai, China)</td>
		</tr>
		<tr>
			<td>Tetracycline</td>
			<td>Sigma</td>
			<td>S-SHS-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Sigma</td>
			<td>SLF-T1503</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Beyotime</td>
			<td>ST825</td>
			<td></td>
		</tr>
		<tr>
			<td>X-gal</td>
			<td>Beyotime</td>
			<td>ST912</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast extract</td>
			<td>Oxoid</td>
			<td>LP0021</td>
			<td></td>
		</tr>
	</tbody>
</table>

screening and identification of small peptides targeting fibroblast growth factor receptor2 using a phage display peptide library

The human Fibroblast Growth Factor Receptor (FGFR) family comprises four members, namely, FGFR1, FGFR2, FGFR3, and FGFR4, that are involved in various biological activities including cell proliferation, survival, migration and differentiation. Several aberrations in the FGFR signaling pathway, owing to mutations or gene amplification events, have been identified in various types of cancers. Hence, recent research has focused on developing strategies involving therapeutic targeting of FGFRs. Current FGFR inhibitors at various stages of pre-clinical and clinical development include either small molecule inhibitors of tyrosine kinases or monoclonal antibodies, with only a few peptide- based inhibitors in the pipeline. Here, we provide a protocol using phage display technology to screen small peptides as antagonists of FGFR2. Briefly, a library of phage-displayed peptides was incubated in a plate coated with FGFR2. Subsequently, unbound phage was washed off by TBST (TBS + 0.1% [v/v] Tween-20), and bound phage was eluted with 0.2 M glycine-HCl buffer (pH 2.2). The eluted phage was further amplified and used as input for the next round of biopanning. Following three rounds of biopanning, the peptide sequences of individual phage clones were identified by DNA sequencing. Finally, the screened peptides were synthesized and analyzed for affinity and biological activity.

Obtaining a high affinity small peptide targeting FGFR2.
To screen phages targeting FGFR2, a Ph.D.-7 library was used in this study. A schematic representation of the workflow is shown in Figure 1. In this process, the number of phage input (PFU) was kept unchanged, whereas the coating concentration of FGFR2 protein was reduced gradually. Results of the phage titer suggested that the number of recovered phages increased gradually, and after 3 roun...

Watch this Scientific Journal Video about Screening and Identification of Small Peptides Targeting Fibroblast Growth Factor Receptor2 using a Phage Display Peptide Library at JoVE.com

Screening and Identification of Small Peptides Targeting Fibroblast Growth Factor Receptor2 using a Phage Display Peptide Library

Herein, we present a detailed protocol for screening small peptides that bind to FGFR2 using a phage display peptide library. We further analyze the affinity of the selected peptides toward FGFR2 in vitro and its ability to suppress cell proliferation.

The human Fibroblast Growth Factor Receptor (FGFR) family comprises four members, namely, FGFR1, FGFR2, FGFR3, and FGFR4, that are involved in various ...

Compared with other methods, this protocol is easier to find out new antagonisters, agonisteres, and allosteric modulators quantitatively and qualitatively without knowing the hydro-dilution structure and formation of the target protein. This protocol is high efficient, easy to handle, economical, and commercially available. Combine this high throughput screening method with ITC analysis, the functional small peptides can be obtained quantitatively and qualitatively.Demonstrating the procedure will be Ying Zhao and Qiang Wang, graduate students from our laboratory. To begin this procedure, prepare a solution of FGFR2 in coating buffer at a concentration of 10 micrograms per milliliter. Add one milliliter of the solution to a 35 square centimeter dish and swirl repeatedly until the surface is completely wet.Incubate overnight at four degrees Celsius with shaking. The next day, pour off the coating solution and add the prepared blocking solution. Incubate at four degrees Celsius for at least one hour, then discard the blocking solution and quickly wash the plate six times with TBST while making sure the dish does not dry out.Reconstitute the original phage library in one milliliter of TBST and add this to the coated dish. Gently rock the plate on a shaker at room temperature for two hours. After this, discard the supernatant and wash the dish 10 times with TBST.Elute the bound phage by adding one milliliter of 0.2 molar glycine HCL to the dish and rocking gently at room temperature for 10 minutes. Transfer the eluent into a sterilized microcentrifuge tube and neutralize it with 100 microliters of one molar Tris-HCL at pH 9.1. First, prewarm the prepared LB and IPTG X-Gal plates at 37 degrees Celsius for at least one hour before use.Using pipette tips with filter cartridges, prepare 100 microliters of tenfold dilutions of the eluent in LB.After the prepared E.coli culture reaches mid-log phase, dispense 200 microliters of the culture into sterilized microcentrifuge tubes one for each eluent dilution. To initiate the infection, add 50 microliters of each dilution to the tubes containing the E.coli culture. Vortex quickly and incubate at room temperature for five minutes.Then use coating sticks to coat the LB and IPTG X-GAL plates with 90 microliters of this mixture. After five minutes, invert the plates and incubate them overnight at 37 degrees Celsius. Count plaques when they appear.To begin, dilute the overnight culture in 20 milliliters of LB in a 250 milliliter Erlenmeyer flask. Add the unamplified eluent and incubate at 37 degrees Celsius with vigorous shaking for 4-1/2 hours. Next, centrifuge the culture at 12, 000 times G and four degrees Celsius for 10 minutes.Transfer the supernatant to a fresh tube. Centrifuge again using the same conditions and discard the pellet. Transfer the upper 80%of the supernatant to a fresh tube and add it to 1/6th volume of 20%polyethylene glycol and 2.5 molar sodium chloride.Allow the phage to precipitate overnight at four degrees Celsius. The next day, centrifuge the precipitated phage at 12, 000 times G and four degrees Celsius for 15 minutes. Discard the supernatant and centrifuge again using the same conditions.Use a pipette to remove the residual supernatant. Resuspend the pellet in one milliliter of TBS and transfer the supernatant to a microcentrifuge tube. Centrifuge at 12, 000 times G and four degrees Celsius for five minutes.Transfer the supernatant to a fresh microcentrifuge tube and precipitate again by adding 1/6th volume of 20%polyethylene glycol and 2.5 molar sodium chloride. Incubate on ice for 15 to 60 minutes. Next, centrifuge at 12, 000 times G and four degrees Celsius for 10 minutes.Discard the supernatant and centrifuge again using the same conditions. Use a pipette to remove the residual supernatant. Resuspend the pellet in 200 microliters of TBS and centrifuge for an additional minute to remove impurities.Then transfer the supernatant to a fresh microcentrifuge tube to obtain the amplified eluent. In this study, the number of phage input is kept unchanged whereas the coating concentration of FGFR2 protein is gradually reduced. Results of the phage titer suggest that the number of recovered phages gradually increases and that after three rounds, there is a 65-fold increase as compared to that of the first round.An ITC experiment is then conducted to measure the affinity of the small peptide to FGFR2. The results indicate that the SP1 peptide has high affinity towards FGFR2. This data demonstrates the efficiency of the screening protocol.To investigate the biological activity of the SP1 peptide, a fibroblast proliferation assay is performed using a CCK-8 kit. BALB/C3T3 are incubated with the SP1 peptide at different concentrations. The results suggest that the SP1 peptide suppresses the growth of the cells.The contamination by wild-type phages has to be avoided here. Make sure to use aerosol-resistant pipette tips. While growth by obtaining phage amplification.This procedure can also be used in screening small peptides that bind to carbohydrates, culture cells, and tissues. Those peptides can be further amplification over diagnostic and targeted

screening-identification-small-peptides-targeting-fibroblast-growth

Research

JoVE Journal

Bioengineering

Therapeutic Gene Delivery and Transfection in Human Pancreatic Cancer Cells using Epidermal Growth Factor Receptor-targeted Gelatin Nanoparticles

More than 32,000 patients are diagnosed with pancreatic cancer in the United States per year and the disease is associated with very high mortality 1. Urgent need exists to develop novel clinically-translatable therapeutic strategies that can improve on the dismal survival statistics of pancreatic cancer patients. Although gene therapy in cancer has shown a tremendous promise, the major challenge is in the development of safe and effective delivery system, which can lead to sustained transgene expression. 
Gelatin is one of the most versatile natural biopolymer, widely used in food and pharmaceutical products. Previous studies from our laboratory have shown that type B gelatin could physical encapsulate DNA, which preserved the supercoiled structure of the plasmid and improved transfection efficiency upon intracellular delivery. By thiolation of gelatin, the sulfhydryl groups could be introduced into the polymer and would form disulfide bond within nanoparticles, which stabilizes the whole complex and once disulfide bond is broken due to the presence of glutathione in cytosol, payload would be released 2-5. Poly(ethylene glycol) (PEG)-modified GENS, when administered into the systemic circulation, provides long-circulation times and preferentially targets to the tumor mass due to the hyper-permeability of the neovasculature by the enhanced permeability and retention effect 6. Studies have shown over-expression of the epidermal growth factor receptor (EGFR) on Panc-1 human pancreatic adenocarcinoma cells 7. In order to actively target pancreatic cancer cell line, EGFR specific peptide was conjugated on the particle surface through a PEG spacer.8
Most anti-tumor gene therapies are focused on administration of the tumor suppressor genes, such as wild-type p53 (wt-p53), to restore the pro-apoptotic function in the cells 9. The p53 mechanism functions as a critical signaling pathway in cell growth, which regulates apoptosis, cell cycle arrest, metabolism and other processes 10. In pancreatic cancer, most cells have mutations in p53 protein, causing the loss of apoptotic activity. With the introduction of wt-p53, the apoptosis could be repaired and further triggers cell death in cancer cells 11. 
Based on the above rationale, we have designed EGFR targeting peptide-modified thiolated gelatin nanoparticles for wt-p53 gene delivery and evaluated delivery efficiency and transfection in Panc-1 cells.

Type B gelatin-based engineered nanovectors system (GENS) was developed for systemic gene delivery and transfection in the treatment of pancreatic cancer. By modification with epidermal growth factor receptor (EGFR) specific peptide on the surface of nanparticles, they could target on EGFR receptor and release plasmid under reducing environment, such as high intracellular glutathione concentrations.

More than 32,000 patients are diagnosed with pancreatic cancer in the United States per year and the disease is associated with very high mortality 1. ...

Generation and Recovery of &beta;-cell Spheroids From Step-growth PEG-peptide Hydrogels

Hydrogels are hydrophilic crosslinked polymers that provide a three-dimensional microenvironment with tissue-like elasticity and high permeability for culturing therapeutically relevant cells or tissues. Hydrogels prepared from poly(ethylene glycol) (PEG) derivatives are increasingly used for a variety of tissue engineering applications, in part due to their tunable and cytocompatible properties. In this protocol, we utilized thiol-ene step-growth photopolymerizations to fabricate PEG-peptide hydrogels for encapsulating pancreatic MIN6 b-cells. The gels were formed by 4-arm PEG-norbornene (PEG4NB) macromer and a chymotrypsin-sensitive peptide crosslinker (CGGYC). The hydrophilic and non-fouling nature of PEG offers a cytocompatible microenvironment for cell survival and proliferation in 3D, while the use of chymotrypsin-sensitive peptide sequence (CGGY&darr;C, arrow indicates enzyme cleavage site, while terminal cysteine residues were added for thiol-ene crosslinking) permits rapid recovery of cell constructs forming within the hydrogel. The following protocol elaborates techniques for: (1) Encapsulation of MIN6 &beta;-cells in thiol-ene hydrogels; (2) Qualitative and quantitative cell viability assays to determine cell survival and proliferation; (3) Recovery of cell spheroids using chymotrypsin-mediated gel erosion; and (4) Structural and functional analysis of the recovered spheroids.

Generation and Recovery of &#946;-cell Spheroids From Step-growth PEG-peptide Hydrogels

The following protocol provides techniques for encapsulating pancreatic &#x03B2;-cells in step-growth PEG-peptide hydrogels formed by thiol-ene photo-click reactions. This material platform not only offers a cytocompatible microenvironment for cell encapsulation, but also permits user-controlled rapid recovery of cell structures formed within the hydrogels.

Hydrogels are hydrophilic crosslinked polymers that provide a three-dimensional  microenvironment with tissue-like elasticity and high permeability for  ...

Observing and Quantifying Fibroblast-mediated Fibrin Gel Compaction

Cells embedded in collagen and fibrin gels attach and exert traction forces on the fibers of the gel. These forces can lead to local and global reorganization and realignment of the gel microstructure. This process proceeds in a complex manner that is dependent in part on the interplay between the location of the cells, the geometry of the gel, and the mechanical constraints on the gel. To better understand how these variables produce global fiber alignment patterns, we use time-lapse differential interference contrast (DIC) microscopy coupled with an environmentally controlled bioreactor to observe the compaction process between geometrically spaced explants (clusters of fibroblasts). The images are then analyzed with a custom image processing algorithm to obtain maps of the strain. The information obtained from this technique can be used to probe the mechanobiology of various cell-matrix interactions, which has important implications for understanding processes in wound healing, disease development, and tissue engineering applications.

Time-lapse microscopy and image processing techniques were used to observe and analyze fibroblast-mediated gel compaction and fibrin fiber realignment in an environmentally controlled bioreactor over a 48 hr&#160;period.

Cells embedded in collagen and fibrin gels attach and exert traction forces on the fibers of the gel. These forces can lead to local and global ...

Electrospinning Growth Factor Releasing Microspheres into Fibrous Scaffolds

This procedure describes a method to fabricate a multifaceted substrate to direct nerve cell growth. This system incorporates mechanical, topographical, adhesive and chemical signals. Mechanical properties are controlled by the type of material used to fabricate the electrospun fibers. In this protocol we use 30% methacrylated Hyaluronic Acid (HA), which has a tensile modulus of ~500 Pa, to produce a soft fibrous scaffold. Electrospinning on to a rotating mandrel produces aligned fibers to create a topographical cue. Adhesion is achieved by coating the scaffold with fibronectin. The primary challenge addressed herein is providing a chemical signal throughout the depth of the scaffold for extended periods. This procedure describes fabricating&#160;poly(lactic-co-glycolic acid) (PLGA) microspheres that contain Nerve Growth Factor (NGF) and directly impregnating the scaffold with these microspheres during the electrospinning process. Due to the harsh production environment, including high sheer forces and electrical charges, protein viability is measured after production. The system provides protein release for over 60 days and has been shown to promote primary nerve cell growth.

This protocol combines electrospinning and microspheres to develop tissue engineered scaffolds to direct neurons. Nerve growth factor was encapsulated within PLGA microspheres and electrospun into Hyaluronic Acid (HA) fibrous scaffolds. The protein bioactivity was tested by seeding the scaffolds with primary chick Dorsal Root Ganglia and culturing for 4-6 days.

This procedure describes a method to fabricate a multifaceted substrate to direct nerve cell growth.  This system incorporates mechanical, topographical, ...

Delivery of Proteins, Peptides or Cell-impermeable Small Molecules into Live Cells by Incubation with the Endosomolytic Reagent dfTAT

Macromolecular delivery strategies typically utilize the endocytic pathway as a route of cellular entry. However, endosomal entrapment severely limits the efficiency with which macromolecules penetrate the cytosolic space of cells. Recently, we have circumvented this problem by identifying the reagent dfTAT, a disulfide bond dimer of the peptide TAT labeled with the fluorophore tetramethylrhodamine. We have generated a fluorescently labeled dimer of the prototypical cell-penetrating peptide (CPP) TAT, dfTAT, which penetrates live cells and reaches the cytosolic space of cells with a particularly high efficiency. Cytosolic delivery of dfTAT is achieved in multiple cell lines, including primary cells. Moreover, delivery does not noticeably impact cell viability, proliferation or gene expression. dfTAT can deliver small molecules, peptides, antibodies, biologically active enzymes and a transcription factor. In this report, we describe the protocols involved in dfTAT synthesis and cellular delivery. The manuscript describes how to control the amount of protein delivered to the cytosolic space of cells by varying the amount of protein administered extracellularly. Finally, the current limitations of this new technology and steps involved in validating delivery are discussed. The described protocols should be extremely useful for cell-based assays as well as for the ex vivo manipulation and reprogramming of cells.

We describe how to deliver proteins and cell-impermeable small molecules into cultured mammalian cells by a simple co-incubation protocol with a reagent that causes endocytic organelles to become leaky.

Macromolecular delivery strategies typically utilize the endocytic pathway as a route of cellular entry. However, endosomal entrapment severely limits the ...

Studying the Stoichiometry of Epidermal Growth Factor Receptor in Intact Cells using Correlative Microscopy

This protocol describes the labeling of epidermal growth factor receptor (EGFR) on COS7 fibroblast cells, and subsequent correlative fluorescence microscopy and environmental scanning electron microscopy (ESEM) of whole cells in hydrated state. Fluorescent quantum dots (QDs) were coupled to EGFR via a two-step labeling protocol, providing an efficient and specific protein labeling, while avoiding label-induced clustering of the receptor. Fluorescence microscopy provided overview images of the cellular locations of the EGFR. The scanning transmission electron microscopy (STEM) detector was used to detect the QD labels with nanoscale resolution. The resulting correlative images provide data of the cellular EGFR distribution, and the stoichiometry at the single molecular level in the natural context of the hydrated intact cell. ESEM-STEM images revealed the receptor to be present as monomer, as homodimer, and in small clusters. Labeling with two different QDs, i.e.,&#160;one emitting at 655 nm and at 800 revealed similar characteristic results.

This protocol describes the labeling of epidermal growth factor receptor (EGFR) on COS7 fibroblast cells, and subsequent correlative light- and electron microscopy of whole cells in hydrated state. The label contained fluorescent quantum dots. The protocol can be used to study the stoichiometry of EGFR at the single molecule level.

This protocol describes the labeling of epidermal growth factor receptor (EGFR) on COS7 fibroblast cells, and subsequent correlative fluorescence ...

A Rapid and Quantitative Fluorimetric Method for Protein-Targeting Small Molecule Drug Screening

We demonstrate a new drug screening method for determining the binding affinity of small drug molecules to a target protein by forming fluorescent gold nanoclusters (Au NCs) within the drug-loaded protein, based on the differential fluorescence signal emitted by the Au NCs. Albumin proteins such as human serum albumin (HSA) and bovine serum albumin (BSA) are selected as the model proteins. Four small molecular drugs (e.g., ibuprofen, warfarin, phenytoin, and sulfanilamide) of different binding affinities to the albumin proteins are tested. It was found that the formation rate of fluorescent Au NCs inside the drug loaded albumin protein under denaturing conditions (i.e., 60 &#176;C or in the presence of urea) is slower than that formed in the pristine protein (without drugs). Moreover, the fluorescent intensity of the as-formed NCs is found to be inversely correlated to the binding affinities of these drugs to the albumin proteins. Particularly, the higher the drug-protein binding affinity, the slower the rate of Au NCs formation, and thus a lower fluorescence intensity of the resultant Au NCs is observed. The fluorescence intensity of the resultant Au NCs therefore provides a simple measure of the relative binding strength of different drugs tested. This method is also extendable to measure the specific drug-protein binding constant (KD) by simply varying the drug content preloaded in the protein at a fixed protein concentration. The measured results match well with the values obtained using other prestige but more complicated methods.

A protocol for small molecular drug screening based on in-situ synthesis of ultrasmall fluorescent gold nanoclusters (Au NCs) using drug-loaded protein as template is presented. This method is simple to determine the binding affinity of drugs to a target protein by a visible fluorescent signal emitted from the protein-templated Au NCs.

We demonstrate a new drug screening method for determining the binding affinity of small drug molecules to a target protein by forming fluorescent gold ...

Polyelectrolyte Complex for Heparin Binding Domain Osteogenic Growth Factor Delivery

During reconstructive bone surgeries, supraphysiological amounts of growth factors are empirically loaded onto scaffolds to promote successful bone fusion. Large doses of highly potent biological agents are required due to growth factor instability as a result of rapid enzymatic degradation as well as carrier inefficiencies in localizing sufficient amounts of growth factor at implant sites. Hence, strategies that prolong the stability of growth factors such as BMP-2/NELL-1, and control their release could actually lower their efficacious dose and thus reduce the need for larger doses during future bone regeneration surgeries. This in turn will reduce side effects and growth factor costs. Self-assembled PECs have been fabricated to provide better control of BMP-2/NELL-1 delivery via heparin binding and further potentiate growth factor bioactivity by enhancing in vivo stability. Here we illustrate the simplicity of PEC fabrication which aids in the delivery of a variety of growth factors during reconstructive bone surgeries.

Self-assembled polyelectrolyte complexes (PEC) fabricated from heparin and protamine were deposited on alginate beads to entrap and regulate the release of osteogenic growth factors. This delivery strategy enables a 20-fold reduction of BMP-2 dose in spinal fusion applications. This article illustrates the benefits and fabrication of PECs.

During reconstructive bone surgeries, supraphysiological amounts of growth factors are empirically loaded onto scaffolds to promote successful bone ...

Initial Evaluation of Antibody-conjugates Modified with Viral-derived Peptides for Increasing Cellular Accumulation and Improving Tumor Targeting

Antibody-conjugates (ACs) modified with virus-derived peptides are a potentially powerful class of tumor cell delivery agents for molecular payloads used in cancer treatment and imaging due to increased cellular accumulation over current ACs. During early AC in vitro development, fluorescence techniques and radioimmunoassays are sufficient for determining intracellular localization, accumulation efficiency, and target cell specificity. Currently, there is no consensus on standardized methods for preparing cells for evaluating AC intracellular accumulation and localization. The initial testing of ACs modified with virus-derived peptides is critical especially if several candidates have been constructed. Determining intracellular accumulation by fluorescence can be affected by background signal from ACs at the cell surface and complicate the interpretation of accumulation. For radioimmunoassays, typically treated cells are fractionated and the radioactivity in different cell compartments measured. However, cell lysis varies from cell to cell and often nuclear and cytoplasmic compartments are not adequately isolated. This can produce misleading data on payload delivery properties. The intravenous injection of radiolabeled virus-derived peptide-modified ACs in tumor bearing mice followed by radionuclide imaging is a powerful method for determining tumor targeting and payload delivery properties at the in vivo phase of development. However, this is a relatively recent advancement and few groups have evaluated virus-derived peptide-modified ACs in this manner. We describe the processing of treated cells to more accurately evaluate virus-derived peptide-modified AC accumulation when using confocal microscopy and radioimmunoassays. Specifically, a method for trypsinizing cells to remove cell surface bound ACs. We also provide a method for improving cellular fractionation. Lastly, this protocol provides an in vivo method using positron emission tomography (PET) for evaluating initial tumor targeting properties in tumor-bearing mice. We use the radioisotope 64Cu (t1/2 = 12.7 h) as an example payload in this protocol.

Viral-derived peptides coupled to antibody-conjugates (ACs) is an approach gaining momentum due to the potential of delivering molecular payloads with increased tumor cell accumulation. Utilizing common methods to evaluate peptide conjugation, AC and payload intracellular accumulation, and tumor targeting, this protocol helps researchers during the key initial development phases.

Antibody-conjugates (ACs) modified with virus-derived peptides are a potentially powerful class of tumor cell delivery agents for molecular payloads used ...

Preparation and Characterization of Novel HDL-mimicking Nanoparticles for Nerve Growth Factor Encapsulation

The objective of this article is to introduce preparation and characterization methods for nerve growth factor (NGF)-loaded, high-density, lipoprotein (HDL)-mimicking nanoparticles (NPs). HDLs are endogenous NPs and have been explored as vehicles for the delivery of therapeutic agents. Various methods have been developed to prepare HDL-mimicking NPs. However, they are generally complicated, time consuming, and difficult for industrial scale-up. In this study, one-step homogenization was used to mix the excipients and form the prototype NPs. NGF is a water-soluble protein of 26 kDa. To facilitate the encapsulation of NGF into the lipid environment of HDL-mimicking NPs, protamine USP was used to form an ion-pair complex with NGF to neutralize the charges on the NGF surface. The NGF/protamine complex was then introduced into the prototype NPs. Apolipoprotein A-I was finally coated on the surface of the NPs. NGF HDL-mimicking NPs showed preferable properties in terms of particle size, size distribution, entrapment efficiency, in vitro release, bioactivity, and biodistribution. With the careful design and exploration of homogenization in HDL-mimicking NPs, the procedure was greatly simplified, and the NPs were made scalable. Moreover, various challenges, such as separating unloaded NGF from the NPs, conducting reliable in vitro release studies, and measuring the bioactivity of the NPs, were overcome.

Simple homogenization was used to prepare novel, high-density, lipoprotein-mimicking nanoparticles to encapsulate nerve growth factor. Challenges, detailed protocols for nanoparticle preparation, in vitro characterization, and in vivo studies are described in this article.

The objective of this article is to introduce preparation and characterization methods for nerve growth factor (NGF)-loaded, high-density, lipoprotein ...