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Sadraeian M, Maleki R, Moraghebi M, Bahrami A. Phage Display Technology in Biomarker Identification with Emphasis on Non-Cancerous Diseases. Molecules 2024; 29:3002. [PMID: 38998954 PMCID: PMC11243120 DOI: 10.3390/molecules29133002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/17/2024] [Accepted: 04/29/2024] [Indexed: 07/14/2024] Open
Abstract
In recent years, phage display technology has become vital in clinical research. It helps create antibodies that can specifically bind to complex antigens, which is crucial for identifying biomarkers and improving diagnostics and treatments. However, existing reviews often overlook its importance in areas outside cancer research. This review aims to fill that gap by explaining the basics of phage display and its applications in detecting and treating various non-cancerous diseases. We focus especially on its role in degenerative diseases, inflammatory and autoimmune diseases, and chronic non-communicable diseases, showing how it is changing the way we diagnose and treat illnesses. By highlighting important discoveries and future possibilities, we hope to emphasize the significance of phage display in modern healthcare.
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Affiliation(s)
- Mohammad Sadraeian
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Reza Maleki
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Mahta Moraghebi
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Abasalt Bahrami
- Department of Chemistry and Biochemistry, Bioengineering, and Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
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2
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Oksanen S, Saarinen R, Korkiakoski A, Lamminmäki U, Huovinen T. Genotyped functional screening of soluble Fab clones enables in-depth analysis of mutation effects. Sci Rep 2023; 13:13107. [PMID: 37567990 PMCID: PMC10421887 DOI: 10.1038/s41598-023-40241-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Monoclonal antibodies (mAbs) and their fragments are widely used in therapeutics, diagnostics and basic research. Although display methods such as phage display offer high-throughput, affinities of individual antibodies need to be accurately measured in soluble format. We have developed a screening platform capable of providing genotyped functional data from a total of 9216 soluble, individual antigen binding fragment (Fab) clones by employing next-generation sequencing (NGS) with hierarchical indexing. Full-length, paired variable domain sequences (VL-VH) are linked to functional screening data, enabling in-depth analysis of mutation effects. The platform was applied to four phage display-selected scFv/Fab screening projects and one site-saturation VH affinity maturation project. Genotyped functional screening simultaneously enabled the identification of affinity improving mutations in the VH domain of Fab 49A3 recognizing Dengue virus non-structural protein 1 (NS1) serotype 2 and informed on VH residue positions which cannot be changed from wild-type without decreasing the affinity. Genotype-based identification revealed to us the extent of intraclonal signal variance inherent to single point screening data, a phenomenon often overlooked in the field. Moreover, genotyped screening eliminated the redundant selection of identical genotypes for further study and provided a new analysis tool to evaluate the success of phage display selections and remaining clonal diversity in the screened repertoires.
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Affiliation(s)
- Sami Oksanen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
| | - Roope Saarinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | | | - Urpo Lamminmäki
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
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Negi P, Heikkilä T, Vuorenpää K, Tuunainen E, Nammas W, Maaniitty T, Knuuti J, Metso J, Lövgren J, Jauhiainen M, Lamminmäki U, Pettersson K, Saraste A. Time-resolved fluorescence based direct two-site apoA-I immunoassays and their clinical application in patients with suspected obstructive coronary artery disease. Front Cardiovasc Med 2022; 9:912578. [PMID: 36312264 PMCID: PMC9614376 DOI: 10.3389/fcvm.2022.912578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Objective High-density lipoprotein (HDL) is a heterogeneous group of subpopulations differing in protein/lipid composition and in their anti-atherogenic function. There is a lack of assays that can target the functionality of HDL particles related to atherosclerosis. The objective of this study was to construct two-site apolipoprotein A-I (apoA-I) assays and to evaluate their clinical performance in patients with suspected obstructive coronary artery disease (CAD). Approach and results Direct two-site apoA-I assays (named 109-121 and 110-525) were developed to identify the presence of apoA-I in the HDL of patients with CAD using apoA-I antibodies as a single-chain variable fragment fused with alkaline phosphatase. ApoA-I109-121 and apoA-I110-525 were measured in 197 patients undergoing coronary computed tomography angiography (CTA) and myocardial positron emission tomography perfusion imaging due to suspected obstructive CAD. Among patients not using lipid-lowering medication (LLM, n = 125), the level of apoA-I110-525 was higher in the presence than in the absence of coronary atherosclerosis [21.88 (15.89-27.44) mg/dl vs. 17.66 (13.38-24.48) mg/dl, P = 0.01)], whereas there was no difference in apoA-I109-121, HDL cholesterol, and apoA-I determined using a polyclonal apoA-I antibody. The levels of apoA-I109-121 and apoA-I110-525 were similar in the presence or absence of obstructive CAD. Among patients not using LLM, apoA-I110-525 adjusted for age and sex identified individuals with coronary atherosclerosis with a similar accuracy to traditional risk factors [area under the curve [AUC] (95% CI): 0.75(0.66-0.84) 0.71 (0.62-0.81)]. However, a combination of apoA-I110-525 with risk factors did not improve the accuracy [AUC (95% CI): 0.73 (0.64-0.82)]. Conclusion Direct two-site apoA-I assays recognizing heterogeneity in reactivity with apoA-I could provide a potential approach to identify individuals at a risk of coronary atherosclerosis. However, their clinical value remains to be studied in larger cohorts.
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Affiliation(s)
- Priyanka Negi
- Department of Life Technologies/Biotechnology, University of Turku, Turku, Finland,*Correspondence: Priyanka Negi
| | - Taina Heikkilä
- Department of Life Technologies/Biotechnology, University of Turku, Turku, Finland
| | - Karoliina Vuorenpää
- Department of Life Technologies/Biotechnology, University of Turku, Turku, Finland
| | - Emilia Tuunainen
- Department of Life Technologies/Biotechnology, University of Turku, Turku, Finland
| | - Wail Nammas
- Heart Center, Turku University Hospital and University of Turku, Turku, Finland,Turku PET Centre, Turku University Hospital, University of Turku, Turku, Finland
| | - Teemu Maaniitty
- Turku PET Centre, Turku University Hospital, University of Turku, Turku, Finland
| | - Juhani Knuuti
- Turku PET Centre, Turku University Hospital, University of Turku, Turku, Finland
| | - Jari Metso
- Minerva Foundation Institute for Medical Research, Biomedicum, Helsinki, Finland,National Institute for Health and Welfare, Genomics and Biobank Unit, Biomedicum 2U, Helsinki, Finland
| | - Janita Lövgren
- Department of Life Technologies/Biotechnology, University of Turku, Turku, Finland
| | - Matti Jauhiainen
- Minerva Foundation Institute for Medical Research, Biomedicum, Helsinki, Finland,National Institute for Health and Welfare, Genomics and Biobank Unit, Biomedicum 2U, Helsinki, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies/Biotechnology, University of Turku, Turku, Finland
| | - Kim Pettersson
- Department of Life Technologies/Biotechnology, University of Turku, Turku, Finland
| | - Antti Saraste
- Heart Center, Turku University Hospital and University of Turku, Turku, Finland,Antti Saraste
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Hietanen E, Tripathi L, Brockmann EC, Merilahti P, Lamminmäki U, Susi P. Isolation and characterization of phage display-derived scFv antibodies against human parechovirus 1 VP0 protein. Sci Rep 2022; 12:13453. [PMID: 35927325 PMCID: PMC9352675 DOI: 10.1038/s41598-022-17678-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
Human parechoviruses (PeVs) are common viruses that are associated with a variety of diseases from mild gastrointestinal and respiratory symptoms to severe central nervous system infections. Until now there has not been antibodies for visualizing parechovirus infection. We used E. coli recombinant PeV-A1-VP0 protein as a target in phage display single chain variable fragment (scFv) antibody library panning. Three rounds of panning allowed identification and isolation of several candidate scFv clones, which tested positive in enzyme-linked immunosorbent assay (ELISA) against VP0. Three scFv clones (scFv-55, -59 and -71) with different CDR-3 sequences were further purified and tested in ELISA, Western blot and immunofluorescence microscopy (IFA) against a set of PeV-A1 isolates and a few isolates representing PeV types 2–6. In IFA, all three scFv binders recognized twenty PeV-A1 isolates. ScFv-55 and -71 also recognized clinical representatives of PeV types 1–6 both in IFA and in capture ELISA, while scFv-59 only recognized PeV-A1, -A2 and -A6. PeV-A1-VP0 (Harris strain) sequence was used to generate a peptide library, which allowed identification of a putative unique conformational antibody epitope with fully conserved flanking regions and a more variable core VVTYDSKL, shared between the scFv antibodies. Sequencing of the VP0 region of virus samples and sequence comparisons against parechoviral sequences in GenBank revealed 107 PeV-A1, -A3, -A8, -A17, -A (untyped) sequences with this exact epitope core sequence, which was most dominant among PeV-A1 isolates. These data suggest the first-time isolation of broad range phage display antibodies against human parechoviruses that may be used in diagnostic antibody development.
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Affiliation(s)
- Eero Hietanen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Lav Tripathi
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Pirjo Merilahti
- Institute of Biomedicine, University of Turku, Turku, Finland.,Biovian Ltd, Turku, Finland
| | - Urpo Lamminmäki
- Department of Biotechnology, University of Turku, Turku, Finland
| | - Petri Susi
- Institute of Biomedicine, University of Turku, Turku, Finland.
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Negi P, Heikkilä T, Tallgren T, Malmi P, Lund J, Sinisalo J, Metso J, Jauhiainen M, Pettersson K, Lamminmäki U, Lövgren J. Three two-site apoA-I immunoassays using phage expressed detector antibodies - Preliminary clinical evaluation with cardiac patients. J Pharm Biomed Anal 2020; 194:113772. [PMID: 33309125 DOI: 10.1016/j.jpba.2020.113772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 11/25/2022]
Abstract
High density lipoproteins (HDL) are a heterogenous group of subpopulations differing in protein/lipid composition and in their anti-atherogenic function. There is a lack of specific and robust assays which can target the functionality of HDL with respect to atherosclerosis. With recently generated CAD HDL targeted, single chain recombinant antibodies (scFvs) we set out to design and optimize apo A-I tests to compare it with conventional HDL-C and apo A-I analyses for diagnosis and risk assessment of coronary artery disease (CAD) and its outcome. Three highly sensitive two-site apo A-I assays: 022-454, 109-121 and 110-525 were optimized. A preliminary clinical evaluation of these assays, after proper sample dilution procedure, was performed using samples derived from 195 chest pain patients (myocardial infarction (MI), n = 86 and non-MI, n = 109), collected at the time of admission and at discharge from hospital (hospital stay ≤ 24 h). The clinical performance of the assays was compared with apo A-I measured with polyclonal anti-apo A-I antibody using conventional ELISA. Apo A-I data was in addition compared with HDL-C concentration of the samples. The concentration of apo A-I was significantly lower in MI patients than in non-MI individuals with assay 022-454 (admission and discharge samples, P < 0.0001 and = 0.004); assay 109-121 (admission and discharge samples, P = 0.04 and 0.0009), and, ELISA based apo A-I test (admission and discharge samples, P = 0.008 and < 0.0001). HDL-C (admission and discharge samples, P = 0.002 and P = 0.01) was also significantly lower in MI patients. In Kaplan- Meier analysis, two-site assay 109-121 assay predicted mortality from admission samples at 1.5 yrs (whole cohort, P = 0.01 and in MI patients, P = 0.05) and at 6 months (whole cohort, P = 0.04). Assay 110-525 predicted mortality at 1.5 yrs from admission samples of non-MI patients (P = 0.01) and at 6 months from whole discharge sample cohort (P = 0.04). Polyclonal anti-apo A-I based conventional assay predicted mortality at 1.5 yrs from admission samples of whole cohort (P = 0.03). Two-site apo A-I assay 022-454 and HDL-C provided no capability of predicting mortality in the whole cohort or any sub-group. In conclusion, two of the tested recombinant apo A-I antibody combinations (sc 109-121 and sc 110-525) display promising outcome to improve diagnosis and prediction of future cardiac events in cardiac patients over polyclonal apo A-I ELISA and HDL-C assays. The noted differences, while interesting, are preliminary and need however to be verified in extensive cohorts of pathological cardiac conditions and healthy controls.
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Affiliation(s)
- Priyanka Negi
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland.
| | - Taina Heikkilä
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
| | - Terhi Tallgren
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
| | - Päivi Malmi
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
| | - Juha Lund
- Heart Center, Turku University Hospital, Finland
| | - Juha Sinisalo
- Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Jari Metso
- Minerva Foundation Institute for Medical Research, Biomedicum, Helsinki, Finland; National Institute for Health and Welfare, Genomics and Biomarkers Unit, Biomedicum, Helsinki, Finland
| | - Matti Jauhiainen
- Minerva Foundation Institute for Medical Research, Biomedicum, Helsinki, Finland; National Institute for Health and Welfare, Genomics and Biomarkers Unit, Biomedicum, Helsinki, Finland
| | - Kim Pettersson
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
| | - Urpo Lamminmäki
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
| | - Janita Lövgren
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
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A Novel Fully Human Agonistic Single Chain Fragment Variable Antibody Targeting Death Receptor 5 with Potent Antitumor Activity In Vitro and In Vivo. Int J Mol Sci 2017; 18:ijms18102064. [PMID: 28953230 PMCID: PMC5666746 DOI: 10.3390/ijms18102064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/03/2017] [Accepted: 09/17/2017] [Indexed: 01/13/2023] Open
Abstract
Agonistic antibodies, which bind specifically to death receptor 5 (DR5), can trigger apoptosis in tumor cells through the extrinsic pathway. In this present study, we describe the use of a phage display to isolate a novel fully human agonistic single chain fragment variable (scFv) antibody, which targets DR5. After five rounds of panning a large (1.2 × 108 clones) phage display library on DR5, a total of over 4000 scFv clones were screened by the phage ELISA. After screening for agonism in a cell-viability assay in vitro, a novel DR5-specific scFv antibody TR2-3 was isolated, which inhibited COLO205 and MDA-MB-231 tumor cell growth without any cross-linking agents. The activity of TR2-3 in inducing apoptosis in cancer cells was evaluated by using an Annexin V-PE apoptosis detection kit in combination with flow cytometry and the Hoechst 33342 and propidium iodide double staining analysis. In addition, the activation of caspase-dependent apoptosis was evaluated by Western blot assays. The results indicated that TR2-3 induced robust apoptosis of the COLO205 and MDA-MB-231 cells in a dose-dependent and time-dependent manner, while it remarkably upregulated the cleavage of caspase-3 and caspase-8. Furthermore, TR2-3 suppressed the tumor growth significantly in the xenograft model. Taken together, these data suggest that TR2-3 exhibited potent antitumor activity both in vitro and in vivo. This work provides a novel human antibody, which might be a promising candidate for cancer therapy by targeting DR5.
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Kimura H, Mikawa S, Mizuguchi C, Horie Y, Morita I, Oyama H, Ohgita T, Nishitsuji K, Takeuchi A, Lund-Katz S, Akaji K, Kobayashi N, Saito H. Immunochemical Approach for Monitoring of Structural Transition of ApoA-I upon HDL Formation Using Novel Monoclonal Antibodies. Sci Rep 2017; 7:2988. [PMID: 28592796 PMCID: PMC5462821 DOI: 10.1038/s41598-017-03208-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/24/2017] [Indexed: 11/24/2022] Open
Abstract
Apolipoprotein A-I (apoA-I) undergoes a large conformational reorganization during remodeling of high-density lipoprotein (HDL) particles. To detect structural transition of apoA-I upon HDL formation, we developed novel monoclonal antibodies (mAbs). Splenocytes from BALB/c mice immunized with a recombinant human apoA-I, with or without conjugation with keyhole limpet hemocyanin, were fused with P3/NS1/1-Ag4-1 myeloma cells. After the HAT-selection and cloning, we established nine hybridoma clones secreting anti-apoA-I mAbs in which four mAbs recognize epitopes on the N-terminal half of apoA-I while the other five mAbs recognize the central region. ELISA and bio-layer interferometry measurements demonstrated that mAbs whose epitopes are within residues 1–43 or 44–65 obviously discriminate discoidal and spherical reconstituted HDL particles despite their great reactivities to lipid-free apoA-I and plasma HDL, suggesting the possibility of these mAbs to detect structural transition of apoA-I on HDL. Importantly, a helix-disrupting mutation of W50R into residues 44–65 restored the immunoreactivity of mAbs whose epitope being within residues 44–65 against reconstituted HDL particles, indicating that these mAbs specifically recognize the epitope region in a random coil state. These results encourage us to develop mAbs targeting epitopes in the N-terminal residues of apoA-I as useful probes for monitoring formation and remodeling of HDL particles.
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Affiliation(s)
- Hitoshi Kimura
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto, 607-8414, Japan.,Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Shiho Mikawa
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto, 607-8414, Japan.,Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Chiharu Mizuguchi
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto, 607-8414, Japan.,Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Yuki Horie
- Department of Bioanalytical Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Izumi Morita
- Department of Bioanalytical Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Hiroyuki Oyama
- Department of Bioanalytical Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Takashi Ohgita
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Kazuchika Nishitsuji
- Department of Molecular Pathology, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Atsuko Takeuchi
- Analytical Laboratory, Kobe Pharmaceutical University, 4-19-1 Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Sissel Lund-Katz
- Lipid Research Group, Gastroenterology, Hepatology and Nutrition Division, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, 19104-4318, USA
| | - Kenichi Akaji
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Norihiro Kobayashi
- Department of Bioanalytical Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Hiroyuki Saito
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Nakauchi-cho, Misasagi, Yamashina-ku, Kyoto, 607-8414, Japan.
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Li T, Huang M, Xiao H, Zhang G, Ding J, Wu P, Zhang H, Sheng J, Chen C. Selection and characterization of specific nanobody against bovine virus diarrhea virus (BVDV) E2 protein. PLoS One 2017; 12:e0178469. [PMID: 28582444 PMCID: PMC5459339 DOI: 10.1371/journal.pone.0178469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/13/2017] [Indexed: 01/15/2023] Open
Abstract
Bovine viral diarrhea-mucosal disease (BVD-MD) is caused by bovine viral diarrhea virus (BVDV), and results in abortion, stillbirth, and fetal malformation in cows. Here, we constructed the phage display vector pCANTAB 5E-VHH and then transformed it into Escherichia coli TG1-competent cells, to construct an initial anti-BVDV nanobody gene library. We obtained a BVDV-E2 antigen epitope bait protein by prokaryotic expression using the nucleotide sequence of the E2 gene of the BVDV-NADL strain published in GenBank. Phage display was used to screen the anti-BVDV nanobody gene library. We successfully constructed a high quality phage display nanobody library, with an initial library capacity of 4.32×105. After the rescue of helper phage, the titer of the phage display nanobody library was 1.3×1011. The BVDV-E2 protein was then expressed in Escherichia coli (DE3), and a 49.5 kDa band was observed with SDS-PAGE analysis that was consistent with the expected nanobody size. Thus, we were able to isolate one nanobody that exhibits high affinity and specificity against BVDV using phage display techniques. This isolated nanobody was then used in Enzyme Linked Immunosorbent Assay and qRT-PCR, and ELISA analyses of BVDV infection of MDBK cells indicated that the nanobodies exhibited good antiviral effect.
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Affiliation(s)
- Tiansen Li
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Meiling Huang
- Shihezi University Library, Shihezi University, Shihezi, Xinjiang, China
| | - Hongran Xiao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Guoqi Zhang
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Jinhua Ding
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Peng Wu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Hui Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Jinliang Sheng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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Lövgren J, Pursiheimo JP, Pyykkö M, Salmi J, Lamminmäki U. Next generation sequencing of all variable loops of synthetic single framework scFv-Application in anti-HDL antibody selections. N Biotechnol 2016; 33:790-796. [PMID: 27450754 DOI: 10.1016/j.nbt.2016.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/01/2016] [Accepted: 07/17/2016] [Indexed: 11/30/2022]
Abstract
Next generation sequencing (NGS) can be applied to monitoring antibody phage display library selection processes to follow the enrichment of each individual antibody clone. Utilising the recent development of the Illumina sequencing platform enabling sequencing up to 2×300bp, we have developed a method to deep sequence all complementarity determining regions (CDRs) in the clones obtained from a synthetic single framework antibody library. This was complemented by an in-house bioinformatics pipeline for efficient analysis of the sequencing results. The method was utilised to study antibody selections against high density lipoprotein (HDL) particles. Sequencing of the output from each selection round enabled extraction of useful information on both the total copy numbers as well as the relative enrichment rates of the clones. Ten antibody clones showing different ranking in terms of frequency were reproduced from synthetic DNA constructs and their capacity to bind HDL was verified by an immunoassay. The method thus facilitates the isolation of clones of interest, and in particular can assist retrieval of less efficiently enriched, yet interesting clones, which are unlikely to be identified by conventional, random colony picking based, screening.
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Affiliation(s)
- Janita Lövgren
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland.
| | - Juha-Pekka Pursiheimo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Mikko Pyykkö
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
| | - Jussi Salmi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Urpo Lamminmäki
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
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