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Haynes WA, Kamath K, Bozekowski J, Baum-Jones E, Campbell M, Casanovas-Massana A, Daugherty PS, Dela Cruz CS, Dhal A, Farhadian SF, Fitzgibbons L, Fournier J, Jhatro M, Jordan G, Klein J, Lucas C, Kessler D, Luchsinger LL, Martinez B, Catherine Muenker M, Pischel L, Reifert J, Sawyer JR, Waitz R, Wunder EA, Zhang M, Iwasaki A, Ko A, Shon JC. High-resolution epitope mapping and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19. Commun Biol 2021; 4:1317. [PMID: 34811480 PMCID: PMC8608966 DOI: 10.1038/s42003-021-02835-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
As Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread, characterization of its antibody epitopes, emerging strains, related coronaviruses, and even the human proteome in naturally infected patients can guide the development of effective vaccines and therapies. Since traditional epitope identification tools are dependent upon pre-defined peptide sequences, they are not readily adaptable to diverse viral proteomes. The Serum Epitope Repertoire Analysis (SERA) platform leverages a high diversity random bacterial display library to identify proteome-independent epitope binding specificities which are then analyzed in the context of organisms of interest. When evaluating immune response in the context of SARS-CoV-2, we identify dominant epitope regions and motifs which demonstrate potential to classify mild from severe disease and relate to neutralization activity. We highlight SARS-CoV-2 epitopes that are cross-reactive with other coronaviruses and demonstrate decreased epitope signal for mutant SARS-CoV-2 strains. Collectively, the evolution of SARS-CoV-2 mutants towards reduced antibody response highlight the importance of data-driven development of the vaccines and therapies to treat COVID-19. Using a high throughput, random bacterial peptide display approach applied to patient serum samples, Haynes, Kamath, Bozekowski et al identify the antigens and epitopes that elicit a SARS-CoV-2 humoral response. They identify differences depending on disease severity and further in silico analysis suggests decreased epitope signal for Q677P but not for D614G mutant SARSCoV-2 strains.
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Affiliation(s)
| | | | | | | | - Melissa Campbell
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Charles S Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Shelli F Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | - John Fournier
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | | | - Jon Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Lauren Pischel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | - Elsio A Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | | | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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2
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Paull ML, Bozekowski JD, Daugherty PS. Mapping antibody binding using multiplexed epitope substitution analysis. J Immunol Methods 2021; 499:113178. [PMID: 34757083 DOI: 10.1016/j.jim.2021.113178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 01/24/2023]
Abstract
A more complete understanding of antibody epitopes would aid the development of diagnostics, therapeutic antibodies, and vaccines. However, current methods for mapping antibody binding to epitopes require a targeted experimental approach, which limits throughput. To address these limitations, we developed Multiplexed Epitope Substitution Analysis (MESA) which can rapidly characterize various distinct epitopes using millions of antibody-binding peptides. We screened peptides from a random 12-mer library that bound to human serum antibody repertoires and determined their sequences using next-generation sequencing (NGS). Computationally, we divided target epitope sequences into overlapping k-mer subsequences and substituted the positions in each k-mer with all 20 amino acids, mimicking a saturation mutagenesis. We then determined enrichments of the substituted k-mers in the screened peptide dataset and used these enrichments to identify substitutions favored for binding at each position in the target epitope, ultimately revealing the precise binding motif. To validate MESA, we determined binding motifs for monoclonal antibodies spiked into serum, recovering the expected binding positions and amino acid preferences. To characterize epitopes bound by a population, we analyzed 50 serum specimens to determine the binding motifs within various target epitopes from common pathogens. Additionally, by analyzing various HSV-1 glycoprotein epitopes, MESA revealed unique binding signatures for HSV-1 seropositive specimens and demonstrated the variability of binding signatures within a population. These results demonstrate that MESA can rapidly identify and characterize binding motifs for an unlimited number of epitopes from a single experiment, accelerating discoveries and enhancing our understanding of antibody-epitope interactions.
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Affiliation(s)
- Michael L Paull
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Joel D Bozekowski
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
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3
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Haynes WA, Kamath K, Waitz R, Daugherty PS, Shon JC. Protein-Based Immunome Wide Association Studies (PIWAS) for the Discovery of Significant Disease-Associated Antigens. Front Immunol 2021; 12:625311. [PMID: 33986742 PMCID: PMC8110919 DOI: 10.3389/fimmu.2021.625311] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/07/2021] [Indexed: 12/17/2022] Open
Abstract
Identification of the antigens associated with antibodies is vital to understanding immune responses in the context of infection, autoimmunity, and cancer. Discovering antigens at a proteome scale could enable broader identification of antigens that are responsible for generating an immune response or driving a disease state. Although targeted tests for known antigens can be straightforward, discovering antigens at a proteome scale using protein and peptide arrays is time consuming and expensive. We leverage Serum Epitope Repertoire Analysis (SERA), an assay based on a random bacterial display peptide library coupled with next generation sequencing (NGS), to power the development of Protein-based Immunome Wide Association Study (PIWAS). PIWAS uses proteome-based signals to discover candidate antibody-antigen epitopes that are significantly elevated in a subset of cases compared to controls. After demonstrating statistical power relative to the magnitude and prevalence of effect in synthetic data, we apply PIWAS to systemic lupus erythematosus (SLE, n=31) and observe known autoantigens, Smith and Ribosomal protein P, within the 22 highest scoring candidate protein antigens across the entire human proteome. We validate the magnitude and location of the SLE specific signal against the Smith family of proteins using a cohort of patients who are positive by predicate anti-Sm tests. To test the generalizability of the method in an additional autoimmune disease, we identified and validated autoantigenic signals to SSB, CENPA, and keratin proteins in a cohort of individuals with Sjogren’s syndrome (n=91). Collectively, these results suggest that PIWAS provides a powerful new tool to discover disease-associated serological antigens within any known proteome.
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Affiliation(s)
| | - Kathy Kamath
- Serimmune, Inc., Santa Barbara, CA, United States
| | | | | | - John C Shon
- Serimmune, Inc., Santa Barbara, CA, United States
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Wang K, Dropulic L, Bozekowski J, Pietz HL, Jegaskanda S, Dowdell K, Vogel JS, Garabedian D, Oestreich M, Nguyen H, Ali MA, Lumbard K, Hunsberger S, Reifert J, Haynes WA, Sawyer JR, Shon JC, Daugherty PS, Cohen JI. Serum and Cervicovaginal Fluid Antibody Profiling in Herpes Simplex Virus (HSV) Seronegative Recipients of the HSV529 Vaccine. J Infect Dis 2021; 224:1509-1519. [PMID: 33718970 DOI: 10.1093/infdis/jiab139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/12/2021] [Indexed: 11/14/2022] Open
Abstract
Previous HSV2 vaccines have not prevented genital herpes. Concerns have been raised about the choice of antigen, the type of antibody induced by the vaccine, and whether antibody is present in the genital tract where infection occurs. We reported results of a trial of an HSV2 replication-defective vaccine, HSV529, that induced serum neutralizing antibody responses in 78% of HSV1 -/HSV2 - vaccine recipients. Here we show that HSV1 -/HSV2 - vaccine recipients developed antibodies to epitopes of several viral proteins; however, fewer antibody epitopes were detected in vaccine recipients compared with naturally infected persons. HSV529 induced antibodies that mediated HSV2-specific NK cell activation. Depletion of gD-binding antibody from sera reduced neutralizing titers by 62% and NK cell activation by 81%. HSV2 gD antibody was detected in cervicovaginal fluid at about one-third the level of that in serum. A vaccine that induces potent serum antibodies transported to the genital tract might reduce HSV genital infection.
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Affiliation(s)
- Kening Wang
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lesia Dropulic
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Harlan L Pietz
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sinthujan Jegaskanda
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kennichi Dowdell
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joshua S Vogel
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Doreen Garabedian
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Makinna Oestreich
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hanh Nguyen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mir A Ali
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keith Lumbard
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Reifert J, Kamath K, Bozekowski J, Lis E, Horn EJ, Granger D, Theel ES, Shon J, Sawyer JR, Daugherty PS. Serum Epitope Repertoire Analysis Enables Early Detection of Lyme Disease with Improved Sensitivity in an Expandable Multiplex Format. J Clin Microbiol 2021; 59:e01836-20. [PMID: 33148704 PMCID: PMC8111119 DOI: 10.1128/jcm.01836-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/27/2020] [Indexed: 12/25/2022] Open
Abstract
Widely employed diagnostic antibody serology for Lyme disease, known as standard two-tier testing (STTT), exhibits insufficient sensitivity in early Lyme disease, yielding many thousands of false-negative test results each year. Given this problem, we applied serum antibody repertoire analysis (SERA), or next-generation sequencing (NGS)-based serology, to discover IgG and IgM antibody epitope motifs capable of detecting Lyme disease-specific antibodies with high sensitivity and specificity. Iterative motif discovery and bioinformatic analysis of epitope repertoires from subjects with Lyme disease (n = 264) and controls (n = 391) yielded a set of 28 epitope motifs representing 20 distinct IgG antibody epitopes and a set of 38 epitope motifs representing 21 distinct IgM epitopes, which performed equivalently in a large validation cohort of STTT-positive samples. In a second validation set from subjects with clinically defined early Lyme disease (n = 119) and controls (n = 257), the SERA Lyme IgG and IgM assay exhibited significantly improved sensitivity relative to STTT (77% versus 62%; Z-test; P = 0.013) and improved specificity (99% versus 97%). Early Lyme disease subjects exhibited significantly fewer reactive epitopes (Mann-Whitney U test; P < 0.0001) relative to subjects with Lyme arthritis. Thus, SERA Lyme IgG and M panels provided increased accuracy in early Lyme disease in a readily expandable multiplex assay format.
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Affiliation(s)
| | | | | | - Ewa Lis
- Serimmune Inc., Goleta, California, USA
| | | | - Dane Granger
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester Minnesota, USA
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester Minnesota, USA
| | - John Shon
- Serimmune Inc., Goleta, California, USA
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6
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Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Ashworth A, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, Feng FY. Autoantibody Landscape in Patients with Advanced Prostate Cancer. Clin Cancer Res 2020; 26:6204-6214. [PMID: 32967941 PMCID: PMC7710628 DOI: 10.1158/1078-0432.ccr-20-1966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/03/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE Autoantibody responses in cancer are of great interest, as they may be concordant with T-cell responses to cancer antigens or predictive of response to cancer immunotherapies. Thus, we sought to characterize the antibody landscape of metastatic castration-resistant prostate cancer (mCRPC). EXPERIMENTAL DESIGN Serum antibody epitope repertoire analysis (SERA) was performed on patient serum to identify tumor-specific neoepitopes. Somatic mutation-specific neoepitopes were investigated by associating serum epitope enrichment scores with whole-genome sequencing results from paired solid tumor metastasis biopsies and germline blood samples. A protein-based immunome-wide association study (PIWAS) was performed to identify significantly enriched epitopes, and candidate serum antibodies enriched in select patients were validated by ELISA profiling. A distinct cohort of patients with melanoma was evaluated to validate the top cancer-specific epitopes. RESULTS SERA was performed on 1,229 serum samples obtained from 72 men with mCRPC and 1,157 healthy control patients. Twenty-nine of 6,636 somatic mutations (0.44%) were associated with an antibody response specific to the mutated peptide. PIWAS analyses identified motifs in 11 proteins, including NY-ESO-1 and HERVK-113, as immunogenic in mCRPC, and ELISA confirmed serum antibody enrichment in candidate patients. Confirmatory PIWAS, Identifying Motifs Using Next-generation sequencing Experiments (IMUNE), and ELISA analyses performed on serum samples from 106 patients with melanoma similarly revealed enriched cancer-specific antibody responses to NY-ESO-1. CONCLUSIONS We present the first large-scale profiling of autoantibodies in advanced prostate cancer, utilizing a new antibody profiling approach to reveal novel cancer-specific antigens and epitopes. Our study recovers antigens of known importance and identifies novel tumor-specific epitopes of translational interest.
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Affiliation(s)
- William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | | | | | | | - Agustin Vega-Crespo
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | | | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Ivan Perez Garcilazo
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Shuang G Zhao
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Matthew Rettig
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Martin Gleave
- University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Primo Lara
- University of California Davis, Davis, California
| | - Kim N Chi
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Department of Urology, University of California Los Angeles, Los Angeles, California
| | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Antoni Ribas
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - David Y Oh
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
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Kamath K, Reifert J, Johnston T, Gable C, Pantazes RJ, Rivera HN, McAuliffe I, Handali S, Daugherty PS. Antibody epitope repertoire analysis enables rapid antigen discovery and multiplex serology. Sci Rep 2020; 10:5294. [PMID: 32210339 PMCID: PMC7093460 DOI: 10.1038/s41598-020-62256-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/11/2020] [Indexed: 01/26/2023] Open
Abstract
The detection of pathogen-specific antibodies remains a cornerstone of clinical diagnostics. Yet, many test exhibit undesirable performance or are completely lacking. Given this, we developed serum epitope repertoire analysis (SERA), a method to rapidly discover conserved, pathogen-specific antigens and their epitopes, and applied it to develop an assay for Chagas disease caused by the protozoan parasite Trypanosoma cruzi. Antibody binding peptide motifs were identified from 28 Chagas repertoires using a bacterial display random 12-mer peptide library and next-generation sequencing (NGS). Thirty-three motifs were selected and mapped to candidate Chagas antigens. In a blinded validation set (n = 72), 30/30 Chagas were positive, 30/30 non-Chagas were negative, and 1/12 Leishmania sp. was positive. After unblinding, a Leishmania cross-reactive epitope was identified and removed from the panel. The Chagas assay exhibited 100% sensitivity (30/30) and specificity (90/90) in a second blinded validation set including individuals with other parasitic infections. Amongst additional epitope repertoires with unknown Chagas serostatus, assay specificity was 99.8% (998/1000). Thus, the Chagas assay achieved a combined sensitivity and specificity equivalent or superior to diagnostic algorithms that rely on three separate tests to achieve high specificity. NGS-based serology via SERA provides an effective approach to discover antigenic epitopes and develop high performance multiplex serological assays.
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Affiliation(s)
- Kathy Kamath
- Serimmune Inc., 150 Castilian Dr., Goleta, CA, 93117, USA
| | - Jack Reifert
- Serimmune Inc., 150 Castilian Dr., Goleta, CA, 93117, USA
| | | | - Cameron Gable
- Serimmune Inc., 150 Castilian Dr., Goleta, CA, 93117, USA
| | - Robert J Pantazes
- Serimmune Inc., 150 Castilian Dr., Goleta, CA, 93117, USA
- Department of Chemical Engineering, Auburn University, Auburn, AL, 36849-5127, USA
| | - Hilda N Rivera
- Centers for Disease Control (CDC)- Division of Parasitic Disease and Malaria, 1600 Clifton Road, MS D-64, Atlanta, GA, 30329-4027, USA
| | - Isabel McAuliffe
- Centers for Disease Control (CDC)- Division of Parasitic Disease and Malaria, 1600 Clifton Road, MS D-64, Atlanta, GA, 30329-4027, USA
| | - Sukwan Handali
- Centers for Disease Control (CDC)- Division of Parasitic Disease and Malaria, 1600 Clifton Road, MS D-64, Atlanta, GA, 30329-4027, USA
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Paull ML, Johnston T, Ibsen KN, Bozekowski JD, Daugherty PS. A general approach for predicting protein epitopes targeted by antibody repertoires using whole proteomes. PLoS One 2019; 14:e0217668. [PMID: 31490930 PMCID: PMC6730857 DOI: 10.1371/journal.pone.0217668] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/22/2019] [Indexed: 12/23/2022] Open
Abstract
Antibodies are essential to functional immunity, yet the epitopes targeted by antibody repertoires remain largely uncharacterized. To aid in characterization, we developed a generalizable strategy to predict antibody-binding epitopes within individual proteins and entire proteomes. Specifically, we selected antibody-binding peptides for 273 distinct sera out of a random library and identified the peptides using next-generation sequencing. To predict antibody-binding epitopes and the antigens from which these epitopes were derived, we tiled the sequences of candidate antigens into short overlapping subsequences of length k (k-mers). We used the enrichment over background of these k-mers in the antibody-binding peptide dataset to predict antibody-binding epitopes. As a positive control, we used this approach, termed K-mer Tiling of Protein Epitopes (K-TOPE), to predict epitopes targeted by monoclonal and polyclonal antibodies of well-characterized specificity, accurately recovering their known epitopes. K-TOPE characterized a commonly targeted antigen from Rhinovirus A, predicting four epitopes recognized by antibodies present in 87% of sera (n = 250). An analysis of 2,908 proteins from 400 viral taxa that infect humans predicted seven enterovirus epitopes and five Epstein-Barr virus epitopes recognized by >30% of specimens. Analysis of Staphylococcus and Streptococcus proteomes similarly predicted 22 epitopes recognized by >30% of specimens. Twelve of these common viral and bacterial epitopes agreed with previously mapped epitopes with p-values < 0.05. Additionally, we predicted 30 HSV2-specific epitopes that were 100% specific against HSV1 in novel and previously reported antigens. Experimentally validating these candidate epitopes could help identify diagnostic biomarkers, vaccine components, and therapeutic targets. The K-TOPE approach thus provides a powerful new tool to elucidate the organisms, antigens, and epitopes targeted by human antibody repertoires.
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Affiliation(s)
- Michael L. Paull
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
- * E-mail: (MLP); (PSD)
| | - Tim Johnston
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
| | - Kelly N. Ibsen
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
| | - Joel D. Bozekowski
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, California, United States of America
- * E-mail: (MLP); (PSD)
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10
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Bozekowski JD, Graham AJ, Daugherty PS. High-titer antibody depletion enhances discovery of diverse serum antibody specificities. J Immunol Methods 2018; 455:1-9. [PMID: 29360471 DOI: 10.1016/j.jim.2018.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/26/2017] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
The human antibody repertoire is a unique repository of information regarding infection, inflammation, and autoimmunity of the past, present, and future. However, antibodies can span vast ranges of concentrations with varying affinities and the repertoire is often heavily polarized by a few species. These complexities lead to difficulties detecting and characterizing low abundance antibody species that may be relevant to disease. We therefore developed a method to selectively remove antibodies from a sample in proportion to the titer of the species prior to analysis, referred to as high-titer depletion (HTD). Peptides from a large random peptide display library were enriched towards binding high-titer antibody species and utilized as binding reagents to deplete the corresponding species from the specimen. HTD enabled the discovery of antibody binding specificities using random peptide library screening with reduced cross-reactivity and background signal and improved coverage of low abundance species. With HTD, three monoclonal antibody species were detected at concentrations at least an order of magnitude lower than without HTD. Additionally, 92 serum antibody specificities were readily discovered from an individual specimen using HTD compared to only 25 specificities without HTD. Parameters affecting the extent of depletion such as the concentration of depleted serum were also adjusted to reproducibly improve the coverage of antibody specificities. These results demonstrate that HTD could be employed for the discovery of rare specificities related to disease and enable extensive characterization of the antibody repertoire. Moreover, the strategy of depletion in proportion to titer could be extended to other applications with complex biological samples to improve discovery.
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Affiliation(s)
- Joel D Bozekowski
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Austin J Graham
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA..
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11
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Ibsen KN, Daugherty PS. Prediction of antibody structural epitopes via random peptide library screening and next generation sequencing. J Immunol Methods 2017; 451:28-36. [PMID: 28827189 PMCID: PMC5698135 DOI: 10.1016/j.jim.2017.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
Next generation sequencing (NGS) is widely applied in immunological research, but has yet to become common in antibody epitope mapping. A method utilizing a 12-mer random peptide library expressed in bacteria coupled with magnetic-based cell sorting and NGS correctly identified >75% of epitope residues on the antigens of two monoclonal antibodies (trastuzumab and bevacizumab). PepSurf, a web-based computational method designed for structural epitope mapping was utilized to compare peptides in libraries enriched for monoclonal antibody (mAb) binders to antigen surfaces (HER2 and VEGF-A). Compared to mimotopes recovered from Sanger sequencing of plated colonies from the same sorting protocol, motifs derived from sets of the NGS data improved epitope prediction as defined by sensitivity and precision, from 18% to 82% and 0.27 to 0.51 for trastuzumab and 47% to 76% and 0.19 to 0.27 for bevacizumab. Specificity was similar for Sanger and NGS, 99% and 97% for trastuzumab and 66% and 67% for bevacizumab. These results indicate that combining peptide library screening with NGS yields epitope motifs that can improve prediction of structural epitopes.
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MESH Headings
- Algorithms
- Amino Acid Motifs
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibody Specificity
- Antineoplastic Agents, Immunological/immunology
- Antineoplastic Agents, Immunological/metabolism
- Bevacizumab/immunology
- Bevacizumab/metabolism
- Binding Sites, Antibody
- Computational Biology
- Databases, Genetic
- Epitope Mapping/methods
- Epitopes
- High-Throughput Nucleotide Sequencing
- Immunomagnetic Separation
- Models, Chemical
- Peptide Library
- Protein Binding
- Receptor, ErbB-2/chemistry
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/immunology
- Receptor, ErbB-2/metabolism
- Structure-Activity Relationship
- Trastuzumab/immunology
- Trastuzumab/metabolism
- Vascular Endothelial Growth Factor A/chemistry
- Vascular Endothelial Growth Factor A/genetics
- Vascular Endothelial Growth Factor A/immunology
- Vascular Endothelial Growth Factor A/metabolism
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Affiliation(s)
- Kelly N Ibsen
- Department of Chemical Engineering, University of California Santa Barbara, CA 93106, USA.
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, CA 93106, USA
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12
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Guerrero JL, Daugherty PS, O'Malley MA. Emerging technologies for protease engineering: New tools to clear out disease. Biotechnol Bioeng 2016; 114:33-38. [PMID: 27497426 DOI: 10.1002/bit.26066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/01/2016] [Indexed: 12/16/2022]
Abstract
Proteases regulate many biological processes through their ability to activate or inactive their target substrates. Because proteases catalytically turnover proteins and peptides, they present unique opportunities for use in biotechnological and therapeutic applications. However, many proteases are capable of cleaving multiple physiological substrates. Therefore their activity, expression, and localization are tightly controlled to prevent unwanted proteolysis. Currently, the use of protease therapeutics has been limited to a handful of proteases with narrow substrate specificities, which naturally limits their toxicity. Wider application of proteases is contingent upon the development of methods for engineering protease selectivity, activity, and stability. Recent advances in the development of high-throughput, bacterial and yeast-based methods for protease redesign have yielded protease variants with novel specificities, reduced toxicity, and increased resistance to inhibitors. Here, we highlight new tools for protease engineering, including methods suitable for the redesign of human secreted proteases, and future opportunities to exploit the catalytic activity of proteases for therapeutic benefit. Biotechnol. Bioeng. 2017;114: 33-38. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jennifer L Guerrero
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106
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13
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Pantazes RJ, Reifert J, Bozekowski J, Ibsen KN, Murray JA, Daugherty PS. Identification of disease-specific motifs in the antibody specificity repertoire via next-generation sequencing. Sci Rep 2016; 6:30312. [PMID: 27481573 PMCID: PMC4969583 DOI: 10.1038/srep30312] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/04/2016] [Indexed: 12/12/2022] Open
Abstract
Disease-specific antibodies can serve as highly effective biomarkers but have been identified for only a relatively small number of autoimmune diseases. A method was developed to identify disease-specific binding motifs through integration of bacterial display peptide library screening, next-generation sequencing (NGS) and computational analysis. Antibody specificity repertoires were determined by identifying bound peptide library members for each specimen using cell sorting and performing NGS. A computational algorithm, termed Identifying Motifs Using Next- generation sequencing Experiments (IMUNE), was developed and applied to discover disease- and healthy control-specific motifs. IMUNE performs comprehensive pattern searches, identifies patterns statistically enriched in the disease or control groups and clusters the patterns to generate motifs. Using celiac disease sera as a discovery set, IMUNE identified a consensus motif (QPEQPF[PS]E) with high diagnostic sensitivity and specificity in a validation sera set, in addition to novel motifs. Peptide display and sequencing (Display-Seq) coupled with IMUNE analysis may thus be useful to characterize antibody repertoires and identify disease-specific antibody epitopes and biomarkers.
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Affiliation(s)
- Robert J Pantazes
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
| | - Jack Reifert
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
| | - Joel Bozekowski
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Kelly N Ibsen
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Joseph A Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
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14
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Luo R, Liu C, Elliott SE, Wang W, Parchim N, Iriyama T, Daugherty PS, Tao L, Eltzschig HK, Blackwell SC, Sibai BM, Kellems RE, Xia Y. Transglutaminase is a Critical Link Between Inflammation and Hypertension. J Am Heart Assoc 2016; 5:JAHA.116.003730. [PMID: 27364991 PMCID: PMC5015405 DOI: 10.1161/jaha.116.003730] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background The pathogenesis of essential hypertension is multifactorial with different underlying mechanisms contributing to disease. We have recently shown that TNF superfamily member 14 LIGHT (an acronym for homologous to lymphotoxins, exhibits inducible expression, and competes with herpes simplex virus glycoprotein D for herpes virus entry mediator, a receptor expressed by T lymphocytes, also known as TNFSF14) induces hypertension when injected into mice. Research reported here was undertaken to examine the role of transglutaminase (TGase) in LIGHT‐induced hypertension. Methods and Results Initial experiments showed that plasma and kidney TGase activity was induced by LIGHT infusion (13.91±2.92 versus 6.75±1.92 mU/mL and 19.86±3.55 versus 12.00±0.97 mU/10 μg) and was accompanied with hypertension (169±7.16 versus 117.17±11.57 mm Hg at day 14) and renal impairment (proteinuria, 61.33±23.21 versus 20.38±9.01 μg/mg; osmolality, 879.57±93.02 versus 1407.2±308.04 mmol/kg). The increase in renal TGase activity corresponded to an increase in RNA for the tissue TGase isoform, termed TG2. Pharmacologically, we showed that LIGHT‐induced hypertension and renal impairment did not occur in the presence of cystamine, a well‐known competitive inhibitor of TGase activity. Genetically, we showed that LIGHT‐mediated induction of TGase, along with hypertension and renal impairment, was dependent on interleukin‐6 and endothelial hypoxia inducible factor‐1α. We also demonstrated that interleukin‐6, endothelial hypoxia inducible factor‐1α, and TGase are required for LIGHT‐induced production of angiotensin receptor agonistic autoantibodies. Conclusions Thus, LIGHT‐induced hypertension, renal impairment, and production of angiotensin receptor agonistic autoantibodies require TGase, most likely the TG2 isoform. Our findings establish TGase as a critical link between inflammation, hypertension, and autoimmunity.
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Affiliation(s)
- Renna Luo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX Department of Nephrology, The First Xiangya Hospital of Central South University, Changsha, Hunan, PRC Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Chen Liu
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX
| | - Serra E Elliott
- Department of Chemical Engineering, University of California, Santa Barbara, CA
| | - Wei Wang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX Department of Nephrology, The First Xiangya Hospital of Central South University, Changsha, Hunan, PRC
| | - Nicholas Parchim
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX
| | - Takayuki Iriyama
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX Department of Obstetrics and Gynecology, University of Tokyo, Japan
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA
| | - Lijian Tao
- Department of Nephrology, The First Xiangya Hospital of Central South University, Changsha, Hunan, PRC
| | - Holger K Eltzschig
- Department of Anesthesiology, University of Colorado-Medical School, Denver, CO
| | - Sean C Blackwell
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Texas Health Science Center at Houston, TX
| | - Baha M Sibai
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Texas Health Science Center at Houston, TX
| | - Rodney E Kellems
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX The University of Texas Graduate School of Biomedical Sciences at Houston, TX
| | - Yang Xia
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX The University of Texas Graduate School of Biomedical Sciences at Houston, TX
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15
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Elliott SE, Parchim NF, Kellems RE, Xia Y, Soffici AR, Daugherty PS. A pre-eclampsia-associated Epstein-Barr virus antibody cross-reacts with placental GPR50. Clin Immunol 2016; 168:64-71. [PMID: 27181993 DOI: 10.1016/j.clim.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/24/2016] [Accepted: 05/05/2016] [Indexed: 12/30/2022]
Abstract
To characterize antibody specificities associated with pre-eclampsia (PE), bacterial displayed peptide library screening and evolution was applied to identify peptide epitopes recognized by plasma antibodies present in women with PE near the time of delivery. Pre-eclamptic women exhibited elevated IgG1 titers towards a peptide epitope KRPSCIGCK within the Epstein-Barr virus nuclear antigen 1 (EBNA-1). EBNA-1 epitope antibodies cross-reacted with a similar epitope within the extracellular N-terminus of the human G protein-coupled receptor, GPR50, expressed in human placental tissue and immortalized placental trophoblast cells. We observed increased antibody binding activity to epitopes from EBNA-1 and GPR50 among women with PE (n=42) compared to healthy-outcome pregnancies (n=43) and nulligravid samples (n=21). The EBNA-1 peptide potently blocked binding of the PE-associated antibody to the GPR50 epitope (IC50=58-81pM). These results reveal the existence of molecular mimicry between EBNA-1 and placental GPR50, supporting a mechanism for IgG1 deposition in the pre-eclamptic placenta.
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Affiliation(s)
- Serra E Elliott
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Nicholas F Parchim
- Departments of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA.
| | - Rodney E Kellems
- Departments of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA.
| | - Yang Xia
- Departments of Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, TX 77030, USA.
| | - Alex R Soffici
- Maternal-Fetal Medicine, Cottage Health System, Santa Barbara, CA 93105, USA.
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
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16
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Abstract
Proteases are attractive as therapeutics given their ability to catalytically activate or inactivate their targets. However, therapeutic use of proteases is limited by insufficient substrate specificity, since off-target activity can induce undesired side-effects. In addition, few methods exist to enhance the activity and specificity of human proteases, analogous to methods for antibody engineering. Given this need, a general methodology termed protease evolution via cleavage of an intracellular substrate (PrECISE) was developed to enable engineering of human protease activity and specificity toward an arbitrary peptide target. PrECISE relies on coexpression of a protease and a peptide substrate exhibiting Förster resonance energy transfer (FRET) within the endoplasmic reticulum of yeast. Use of the FRET reporter substrate enabled screening large protease libraries using fluorescence activated cell sorting for the activity of interest. To evolve a human protease that selectively cleaves within the central hydrophobic core (KLVF↓F↓AED) of the amyloid beta (Aβ) peptide, PrECISE was applied to human kallikrein 7, a protease with Aβ cleavage activity but broad selectivity, with a strong preference for tyrosine (Y) at P1. This method yielded a protease variant which displayed up to 30-fold improvements in Aβ selectivity mediated by a reduction in activity toward substrates containing tyrosine. Additionally, the increased selectivity of the variant led to reduced toxicity toward PC12 neuronal-like cells and 16-1000-fold improved resistance to wild-type inhibitors. PrECISE thus provides a powerful high-throughput capability to redesign human proteases for therapeutic use.
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Affiliation(s)
- Jennifer L. Guerrero
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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17
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Liu C, Luo R, Elliott SE, Wang W, Parchim NF, Iriyama T, Daugherty PS, Blackwell SC, Sibai BM, Kellems RE, Xia Y. Elevated Transglutaminase Activity Triggers Angiotensin Receptor Activating Autoantibody Production and Pathophysiology of Preeclampsia. J Am Heart Assoc 2015; 4:JAHA.115.002323. [PMID: 26675250 PMCID: PMC4845265 DOI: 10.1161/jaha.115.002323] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background Preeclampsia (PE) is a life‐threatening hypertensive disorder of pregnancy associated with autoantibodies, termed AT1‐AA, that activate the AT1 angiotensin receptor. Although the pathogenic nature of these autoantibodies has been extensively studied, little is known about the molecular cause of their generation. Methods and Results Here we show that tissue transglutaminase (TG2), an enzyme that conducts posttranslational modification of target proteins, directly modified the 7‐amino acid (7‐aa) epitope peptide that localizes to the second extracellular loop of the AT1 receptor. These findings led us to further discover that plasma transglutaminase activity was induced and contributed to the production of AT1‐AA and disease development in an experimental model of PE induced by injection of LIGHT, a tumor necrosis factor superfamily member. Key features of PE were regenerated by adoptive transfer of purified IgG from LIGHT‐injected pregnant mice and blocked by the 7‐amino acid epitope peptide. Translating our mouse research to humans, we found that plasma transglutaminase activity was significantly elevated in PE patients and was positively correlated with AT1‐AA levels and PE features. Conclusions Overall, we provide compelling mouse and human evidence that elevated transglutaminase underlies AT1‐AA production in PE and highlight novel pathogenic biomarkers and innovative therapeutic possibilities for the disease.
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Affiliation(s)
- Chen Liu
- Departments of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX (C.L., R.L., W.W., N.F.P., T.I., R.E.K., Y.X.)
| | - Renna Luo
- Departments of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX (C.L., R.L., W.W., N.F.P., T.I., R.E.K., Y.X.) Nephrology Department, Xiangya Hospital, Hunan, China (R.L., W.W.) Department of Nephrology, The First Affiliated Hospital of Dalian Medical University, Dalian, China (R.L.)
| | - Serra E Elliott
- Department of Chemical Engineering, University of California, Santa Barbara, CA (S.E.E., P.S.D., Y.X.)
| | - Wei Wang
- Departments of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX (C.L., R.L., W.W., N.F.P., T.I., R.E.K., Y.X.) Nephrology Department, Xiangya Hospital, Hunan, China (R.L., W.W.)
| | - Nicholas F Parchim
- Departments of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX (C.L., R.L., W.W., N.F.P., T.I., R.E.K., Y.X.)
| | - Takayuki Iriyama
- Departments of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX (C.L., R.L., W.W., N.F.P., T.I., R.E.K., Y.X.) Department of Obstetrics and Gynecology, University of Tokyo, Japan (T.I.)
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA (S.E.E., P.S.D., Y.X.)
| | - Sean C Blackwell
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Texas Health Science Center at Houston, TX (S.C.B., B.M.S.)
| | - Baha M Sibai
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Texas Health Science Center at Houston, TX (S.C.B., B.M.S.)
| | - Rodney E Kellems
- Departments of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX (C.L., R.L., W.W., N.F.P., T.I., R.E.K., Y.X.) The University of Texas Graduate School of Biomedical Sciences at Houston, TX (R.E.K., Y.X.)
| | - Yang Xia
- Departments of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, TX (C.L., R.L., W.W., N.F.P., T.I., R.E.K., Y.X.) The University of Texas Graduate School of Biomedical Sciences at Houston, TX (R.E.K., Y.X.) Department of Chemical Engineering, University of California, Santa Barbara, CA (S.E.E., P.S.D., Y.X.)
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18
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Shropshire TD, Reifert J, Rajagopalan S, Baker D, Feinstein SC, Daugherty PS. Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro. Biol Chem 2014; 395:109-18. [PMID: 23989112 DOI: 10.1515/hsz-2013-0230] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 08/27/2013] [Indexed: 12/23/2022]
Abstract
The gradual accumulation and assembly of β-amyloid (Aβ) peptide into neuritic plaques is a major pathological hallmark of Alzheimer disease (AD). Proteolytic degradation of Aβ is an important clearance mechanism under normal circumstances, and it has been found to be compromised in those with AD. Here, the extended substrate specificity and Aβ-degrading capacity of kallikrein 7 (KLK7), a serine protease with a unique chymotrypsin-like specificity, was characterized. Preferred peptide substrates of KLK7 identified using a bacterial display substrate library were found to exhibit a consensus motif of RXΦ(Y/F)↓(Y/F)↓(S/A/G/T) or RXΦ(Y/F)↓(S/T/A) (Φ=hydrophobic), which is remarkably similar to the hydrophobic core motif of Aβ (K16L17V18F19F20 A21) that is largely responsible for aggregation propensity. KLK7 was found to cleave after both Phe residues within the core of Aβ42 in vitro, thereby inhibiting Aβ fibril formation and promoting the degradation of preformed fibrils. Finally, the treatment of Aβ oligomer preparations with KLK7, but not inactive pro-KLK7, significantly reduced Aβ42-mediated toxicity to rat hippocampal neurons to the same extent as the known Aβ-degrading protease insulin-degrading enzyme (IDE). Taken together, these results indicate that KLK7 possesses an Aβ-degrading capacity that can ameliorate the toxic effects of the aggregated peptide in vitro.
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19
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Desnoyers LR, Vasiljeva O, Richardson JH, Yang A, Menendez EEM, Liang TW, Wong C, Bessette PH, Kamath K, Moore SJ, Sagert JG, Hostetter DR, Han F, Gee J, Flandez J, Markham K, Nguyen M, Krimm M, Wong KR, Liu S, Daugherty PS, West JW, Lowman HB. Tumor-specific activation of an EGFR-targeting probody enhances therapeutic index. Sci Transl Med 2014; 5:207ra144. [PMID: 24132639 DOI: 10.1126/scitranslmed.3006682] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Target-mediated toxicity constitutes a major limitation for the development of therapeutic antibodies. To redirect the activity of antibodies recognizing widely distributed targets to the site of disease, we have applied a prodrug strategy to create an epidermal growth factor receptor (EGFR)-directed Probody therapeutic-an antibody that remains masked against antigen binding until activated locally by proteases commonly active in the tumor microenvironment. In vitro, the masked Probody showed diminished antigen binding and cell-based activities, but when activated by appropriate proteases, it regained full activity compared to the parental anti-EGFR antibody cetuximab. In vivo, the Probody was largely inert in the systemic circulation of mice, but was activated within tumor tissue and showed antitumor efficacy that was similar to that of cetuximab. The Probody demonstrated markedly improved safety and increased half-life in nonhuman primates, enabling it to be dosed safely at much higher levels than cetuximab. In addition, we found that both Probody-responsive xenograft tumors and primary tumor samples from patients were capable of activating the Probody ex vivo. Probodies may therefore improve the safety profile of therapeutic antibodies without compromising efficacy of the parental antibody and may enable the wider use of empowered antibody formats such as antibody-drug conjugates and bispecifics.
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Affiliation(s)
- Luc R Desnoyers
- CytomX Therapeutics Inc., 343 Oyster Point Boulevard, Suite 100, South San Francisco, CA 94080, USA
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20
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Kaukinen K, Daugherty PS. Letter: nonresponsive coeliac disease and evaluation of the strictness of a gluten-free diet - authors' reply. Aliment Pharmacol Ther 2014; 39:1242. [PMID: 24735144 DOI: 10.1111/apt.12729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 12/08/2022]
Affiliation(s)
- K Kaukinen
- Department of Gastroenterology and Alimentary Tract Surgery, Univeristy of Tampere, Tampere, Finland
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21
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Spatola BN, Kaukinen K, Collin P, Mäki M, Kagnoff MF, Daugherty PS. Persistence of elevated deamidated gliadin peptide antibodies on a gluten-free diet indicates nonresponsive coeliac disease. Aliment Pharmacol Ther 2014; 39:407-17. [PMID: 24392888 PMCID: PMC3962785 DOI: 10.1111/apt.12603] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 09/18/2013] [Accepted: 12/11/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Histologically nonresponsive coeliac disease (NRCD) is a potentially serious condition diagnosed during the follow-up of coeliac disease (CD) when patients have persistent villous atrophy despite following a gluten-free diet (GFD). AIM As current assessments of recovery are limited to invasive and costly serial duodenal biopsies, we sought to identify antibody biomarkers for CD patients that do not respond to traditional therapy. METHODS Bacterial display peptide libraries were screened by flow cytometry to identify epitopes specifically recognised by antibodies from patients with NRCD, but not by antibodies from responsive CD patients. Deamidated gliadin was confirmed to be the antigen mimicked by library peptides using ELISA with sera from NRCD (n = 15) and responsive CD (n = 45) patients on a strict GFD for at least 1 year. RESULTS The dominant consensus epitope sequence identified by unbiased library screening QPxx(A/P)FP(E/D) was highly similar to reported deamidated gliadin peptide (dGP) B-cell epitopes. Measurement of anti-dGP IgG titre by ELISA discriminated between NRCD and responsive CD patients with 87% sensitivity and 89% specificity. Importantly, dGP antibody titre correlated with the severity of mucosal damage indicating that IgG dGP titres may be useful to monitor small intestinal mucosal recovery on a GFD. CONCLUSIONS The finding of increased levels of anti-dGP IgG antibodies in CD patients on strict GFDs effectively identifies patients with NRCD. Finally, anti-dGP IgG assays may be useful to monitor mucosal damage and histological improvement in CD patients on a strict GFD.
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Affiliation(s)
- Bradley N. Spatola
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Katri Kaukinen
- School of Medicine, University of Tampere and Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland,Department of Medicine, Seinäjoki Central Hospital, Seinäjoki, Finland
| | - Pekka Collin
- School of Medicine, University of Tampere and Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Markku Mäki
- Center for Child Health Research, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Martin F. Kagnoff
- Laboratory of Mucosal Immunology, Departments of Medicine and Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA,Correspondence ; Postal: Department of Chemical Engineering; Engineering II, Rm 3357; University of California, Santa Barbra; Santa Barbara, CA 93106-5080; Phone: (805) 893-2610
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22
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Abstract
The presence of maternal autoantibodies has been previously associated with preeclampsia, although the composition of the antibody repertoire in preeclampsia has not been well characterized. Given this, we applied a bacterial display peptide library to identify peptides that preferentially react with plasma antibodies from patients with preeclampsia (n=15) versus healthy-outcome pregnancies (n=18). Screening using fluorescence-activated cell sorting identified 38 peptides that preferentially bind to antibodies from individuals with preeclampsia. These preeclampsia-specific peptides possessed similar motifs of R(G)/S(G)/-WW(G)/S, RWW(G)/S, or WGWGXX(R)/K distinct from the angiotensin II type 1 receptor epitope AFHYESQ. Seven library-isolated peptides and a cell surface-displayed angiotensin II type 1 receptor epitope were used to construct a diagnostic algorithm with a training set of 18 new preeclamptic and 22 healthy-outcome samples from geographically distinct cohorts. Cross-validation within the training group resulted in averaged areas underneath a receiver operating characteristic curve of 0.78 and 0.72 with and without the known receptor epitope, respectively. In a small validation set (12 preeclamptic; 8 healthy), the algorithm consisting only of library-isolated peptides correctly classified 10 preeclamptic and 6 healthy samples using a predefined cutoff that achieved 61% sensitivity (95% confidence interval, 36%-83%) at 95% specificity (95% confidence interval, 77%-100%) in training set (n=40) cross-validation. Our results indicate that antibodies with specificities other than anti-angiotensin II type 1 receptor are prevalent in preeclampsia patients and may be useful as diagnostic biomarkers.
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Affiliation(s)
- Serra E Elliott
- Engineering II, Room 3357, University of California, Santa Barbara, CA 93106-5080.
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23
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Henriques ST, Thorstholm L, Huang YH, Getz JA, Daugherty PS, Craik DJ. A novel quantitative kinase assay using bacterial surface display and flow cytometry. PLoS One 2013; 8:e80474. [PMID: 24260399 PMCID: PMC3829888 DOI: 10.1371/journal.pone.0080474] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/14/2013] [Indexed: 02/04/2023] Open
Abstract
The inhibition of tyrosine kinases is a successful approach for the treatment of cancers and the discovery of kinase inhibitor drugs is the focus of numerous academic and pharmaceutical laboratories. With this goal in mind, several strategies have been developed to measure kinase activity and to screen novel tyrosine kinase inhibitors. Nevertheless, a general non-radioactive and inexpensive approach, easy to implement and adapt to a range of applications, is still missing. Herein, using Bcr-Abl tyrosine kinase, an oncogenic target and a model protein for cancer studies, we describe a novel cost-effective high-throughput screening kinase assay. In this approach, named the BacKin assay, substrates displayed on a Bacterial cell surface are incubated with Kinase and their phosphorylation is examined and quantified by flow cytometry. This approach has several advantages over existing approaches, as using bacteria (i.e. Escherichia coli) to display peptide substrates provides a self renewing solid support that does not require laborious chemical strategies. Here we show that the BacKin approach can be used for kinetic and mechanistic studies, as well as a platform to characterize and identify small-molecule or peptide-based kinase inhibitors with potential applications in drug development.
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Affiliation(s)
- Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
| | - Louise Thorstholm
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Jennifer A. Getz
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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24
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Zdzalik M, Kalinska M, Wysocka M, Stec-Niemczyk J, Cichon P, Stach N, Gruba N, Stennicke HR, Jabaiah A, Markiewicz M, Kedracka-Krok S, Wladyka B, Daugherty PS, Lesner A, Rolka K, Dubin A, Potempa J, Dubin G. Biochemical and structural characterization of SplD protease from Staphylococcus aureus. PLoS One 2013; 8:e76812. [PMID: 24130791 PMCID: PMC3793935 DOI: 10.1371/journal.pone.0076812] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/29/2013] [Indexed: 01/11/2023] Open
Abstract
Staphylococcus aureus is a dangerous human pathogen. A number of the proteins secreted by this bacterium are implicated in its virulence, but many of the components of its secretome are poorly characterized. Strains of S. aureus can produce up to six homologous extracellular serine proteases grouped in a single spl operon. Although the SplA, SplB, and SplC proteases have been thoroughly characterized, the properties of the other three enzymes have not yet been investigated. Here, we describe the biochemical and structural characteristics of the SplD protease. The active enzyme was produced in an Escherichia coli recombinant system and purified to homogeneity. P1 substrate specificity was determined using a combinatorial library of synthetic peptide substrates showing exclusive preference for threonine, serine, leucine, isoleucine, alanine, and valine. To further determine the specificity of SplD, we used high-throughput synthetic peptide and cell surface protein display methods. The results not only confirmed SplD preference for a P1 residue, but also provided insight into the specificity of individual primed- and non-primed substrate-binding subsites. The analyses revealed a surprisingly narrow specificity of the protease, which recognized five consecutive residues (P4-P3-P2-P1-P1’) with a consensus motif of R-(Y/W)-(P/L)-(T/L/I/V)↓S. To understand the molecular basis of the strict substrate specificity, we crystallized the enzyme in two different conditions, and refined the structures at resolutions of 1.56 Å and 2.1 Å. Molecular modeling and mutagenesis studies allowed us to define a consensus model of substrate binding, and illustrated the molecular mechanism of protease specificity.
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Affiliation(s)
- Michal Zdzalik
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Magdalena Kalinska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Justyna Stec-Niemczyk
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Przemyslaw Cichon
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Natalia Stach
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Natalia Gruba
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Abeer Jabaiah
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California, United States of America
| | - Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California, United States of America
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Adam Dubin
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Center of Oral Health and Systemic Disease, School of Dentistry, University of Louisville, Louisville, Kentucky, United States of America
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- Malopolska Centre of Biotechnology, Krakow, Poland
- * E-mail:
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25
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Getz JA, Cheneval O, Craik DJ, Daugherty PS. Design of a cyclotide antagonist of neuropilin-1 and -2 that potently inhibits endothelial cell migration. ACS Chem Biol 2013; 8:1147-54. [PMID: 23537207 DOI: 10.1021/cb4000585] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neuropilin-1 and -2 are critical regulators of angiogenesis, lymphangiogenesis, and cell survival as receptors for multiple growth factors. Disulfide-rich peptides that antagonize the growth factor receptors neuropilin-1 and neuropilin-2 were developed using bacterial display libraries. Peptide ligands specific for the VEGFA binding site on neuropilin-1 were identified by screening a library of disulfide-rich peptides derived from the thermostable, protease-resistant cyclotide kalata B1. First generation ligands were subjected to one cycle of affinity maturation to yield acyclic peptides with affinities of 40-60 nM and slow dissociation rate constants (∼1 × 10(-3) s(-1)). Peptides exhibited equivalent affinities for human and mouse neuropilin-1 and cross-reacted with human neuropilin-2 with lower affinity. A C-to-N cyclized variant (cyclotide) of one neuropilin ligand retained high affinity, exhibited increased protease resistance, and conferred improved potency for inhibiting endothelial cell migration in vitro (EC50 ≈ 100 nM). These results demonstrate that potent, target-specific cyclotides can be created by evolutionary design and that backbone cyclization can confer improved pharmacological properties.
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Affiliation(s)
- Jennifer A. Getz
- Department of Chemical Engineering, University of California, Santa Barbara, California
93106, United States
| | - Olivier Cheneval
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, California
93106, United States
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26
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Jabaiah AM, Getz JA, Witkowski WA, Hardy JA, Daugherty PS. Identification of protease exosite-interacting peptides that enhance substrate cleavage kinetics. Biol Chem 2013; 393:933-41. [PMID: 22944693 DOI: 10.1515/hsz-2012-0162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/06/2012] [Indexed: 11/15/2022]
Abstract
Many peptidases are thought to require non-active site interaction surfaces, or exosites, to recognize and cleave physiological substrates with high specificity and catalytic efficiency. However, the existence and function of protease exosites remain obscure owing to a lack of effective methods to identify and characterize exosite-interacting substrates. To address this need, we modified the cellular libraries of peptide substrates (CLiPS) methodology to enable the discovery of exosite-interacting peptide ligands. Invariant cleavage motifs recognized by the active sites of thrombin and caspase-7 were displayed on the outer surface of bacteria adjacent to a candidate exosite-interacting peptide. Exosite peptide libraries were then screened for ligands that accelerate cleavage of the active site recognition motif using two-color flow cytometry. Exosite CLiPS (eCLiPS) identified exosite-binding peptides for thrombin that were highly similar to a critical exosite interaction motif in the thrombin substrate, protease-activated receptor 1. Protease activity probes incorporating exosite-binding peptides were cleaved ten-fold faster than substrates without exosite ligands, increasing their sensitivity to thrombin activity in vitro. For comparison, screening with caspase-7 yielded peptides that modestly enhanced (two-fold) substrate cleavage rates. The eCLiPS method provides a new tool to profile the ligand specificity of protease exosites and to develop improved substrates.
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Affiliation(s)
- Abeer M Jabaiah
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
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27
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Spatola BN, Murray JA, Kagnoff M, Kaukinen K, Daugherty PS. Antibody repertoire profiling using bacterial display identifies reactivity signatures of celiac disease. Anal Chem 2013; 85:1215-22. [PMID: 23234559 PMCID: PMC3903178 DOI: 10.1021/ac303201d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A general strategy to identify serum antibody specificities associated with a given disease state and peptide reagents for their detection was developed using bacterial display peptide libraries and multiparameter flow cytometry (MPFC). Using sera from patients with celiac disease (CD) (n = 45) or healthy subjects (n = 40), bacterial display libraries were screened for peptides that react specifically with antibodies from CD patients and not with those from healthy patients. The libraries were screened for peptides that simultaneously cross-react with CD patient antibodies present in two separate patient groups labeled with spectrally distinct fluorophores but do not react with unlabeled non-CD antibodies, thus affording a quantitative separation. A panel of six unique peptide sequences yielded 85% sensitivity and 91% specificity (AUC = 0.91) on a set of 60 samples not used for discovery, using leave-one-out cross-validation. Individual peptides were dissimilar with known CD-specific antigens tissue transglutaminase (tTG) and deamidated gliadin, and the classifier accuracy was independent of anti-tTG antibody titer. These results demonstrate that bacterial display/MPFC provides a highly effective tool for the unbiased discovery of disease-associated antibody specificities and peptide reagents for their detection that may have broad utility for diagnostic development.
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Affiliation(s)
- Bradley N. Spatola
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Joseph A. Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Martin Kagnoff
- Laboratory of Mucosal Immunology, Department of Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, United States
| | - Katri Kaukinen
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
- Medical School, University of Tampere, Tampere, Finland
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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28
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Elliott SE, Soffici AR, Daugherty PS. OS042. Discovery and characterization of antibody biomarkers ofpre-eclampsia and reagents for their detection. Pregnancy Hypertens 2012; 2:199-200. [PMID: 26105256 DOI: 10.1016/j.preghy.2012.04.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION The effective management of pre-eclampsia (PE), a complex condition affecting 5% of pregnancies [1], would benefit from a clear diagnostic assay. Due to this need, great interest lies in the development and validation of objective biomarkers, among which antibodies remain attractive given their amplification by the immune system, stability, and current clinical use. Although several recent studies lend support to the idea that autoantibodies against the angiotensin II AT1 receptor (AT1-AAs) could be involved in PE [1], their presence is not highly specific for PE as measured by cell-based assays for AT1 agonism [2]. Given these results, we hypothesized that additional antibody biomarkers may exist in PE, and that a small panel of such biomarkers could provide an effective diagnostic tool. Furthermore, development of a simple binding assay will facilitate AT1-AA detection for larger-scale studies, while identifying other antibody biomarker(s) would enhance understanding of the immune component to PE pathogenesis. OBJECTIVES The primary objective of this study was to identify a panel of peptide reagents that preferentially bind PE patients' serum antibodies. In addition, we sought to measure the frequency of AT1-AAs in a new patient cohort using a simplified assay. METHODS Plasma samples were obtained from normal-outcome pregnancies (n=28) as well as PE patients (n=25) and enriched for the antibody fraction. The seven amino acid AT1-AA epitope [1] was expressed on the surface of E. coli for reactivity analysis by flow cytometry. A bacteria-displayed linear peptide library was screened against the antibody repertoires using a unique method of fluorescence activated cell sorting (FACS) to isolate peptides that react with multiple patients and show little reactivity with normal-outcome pregnancies. FACS analysis was used to measure individual peptide reactivity, and statistical analyses included a Student's t-test and nonparametric tests to compare the means, medians, and normal scores. RESULTS Using this simple binding assay, AT1-AAs were detected in a majority of PE patients and more rarely in normal-outcome pregnancies. Among the isolated peptide mimics, several unique peptides demonstrated significantly (p<0.03) higher reactivity with PE patients than with control samples but showed no sequence homology to the known AT1 epitope. Not only did our peptides perform well with the original set of samples used for discovery, but these peptides also reacted with antibodies from a small set of new PE (n=10) sera but not from new normal-outcome (n=10) pregnancies. CONCLUSION Peptides distinct from the AT1 epitope and identified by library screening exhibited potential diagnostic utility for PE, suggesting that a panel of such peptides might provide a novel diagnostic test to distinguish PE from other conditions with similar symptoms. Also, this study demonstrated AT1-AA presence in an independent patient cohort with a simple binding assay, which can be easily expanded to evaluate larger cohorts.
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Affiliation(s)
- S E Elliott
- Chemical Engineering Department, University of California, Santa Barbara, United States
| | - A R Soffici
- Maternal-Fetal Medicine Unit, Cottage Health System, Santa Barbara, United States
| | - P S Daugherty
- Chemical Engineering Department, University of California, Santa Barbara, United States
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29
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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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30
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Abstract
Peptides within the knottin family have been shown to possess inherent stability, making them attractive scaffolds for the development of therapeutic and diagnostic agents. Given its remarkable stability to proteases, the cyclic peptide kalata B1 was employed as a scaffold to create a large knottin library displayed on the surface of E. coli. A library exceeding 10(9) variants was constructed by randomizing seven amino acids within a loop of the kalata B1 scaffold and screened using fluorescence-activated cell sorting to identify peptide ligands specific for the active site of human thrombin. Refolded thrombin binders exhibited high nanomolar affinities in solution and slow dissociation rates and were able to inhibit thrombin's enzymatic activity. Importantly, 80% of a knottin-based thrombin inhibitor remained intact after a 2 h incubation both with trypsin and with chymotrypsin, demonstrating that modifying the kalata B1 sequence did not compromise its stability properties. In addition, the knottin variant mediated 20-fold enhanced affinity for thrombin, when compared to the same seven residue binding epitope constrained by a single disulfide bond. Our results indicate that peptide libraries derived from the kalata B1 scaffold can yield high-affinity protein ligands that retain the remarkable protease resistance associated with the parent scaffold. More generally, this strategy may prove useful in the development of stable peptide ligands suitable for in vivo applications.
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Affiliation(s)
- Jennifer A. Getz
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
| | - Jeffrey J. Rice
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106
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31
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Kalińska M, Kantyka T, Greenbaum DC, Larsen KS, Władyka B, Jabaiah A, Bogyo M, Daugherty PS, Wysocka M, Jaros M, Lesner A, Rolka K, Schaschke N, Stennicke H, Dubin A, Potempa J, Dubin G. Substrate specificity of Staphylococcus aureus cysteine proteases--Staphopains A, B and C. Biochimie 2011; 94:318-27. [PMID: 21802486 DOI: 10.1016/j.biochi.2011.07.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
Abstract
Human strains of Staphylococcus aureus secrete two papain-like proteases, staphopain A and B. Avian strains produce another homologous enzyme, staphopain C. Animal studies suggest that staphopains B and C contribute to bacterial virulence, in contrast to staphopain A, which seems to have a virulence unrelated function. Here we present a detailed study of substrate preferences of all three proteases. The specificity of staphopain A, B and C substrate-binding subsites was mapped using different synthetic substrate libraries, inhibitor libraries and a protein substrate combinatorial library. The analysis demonstrated that the most efficiently hydrolyzed sites, using Schechter and Berger nomenclature, comprise a P2-Gly↓Ala(Ser) sequence motif, where P2 distinguishes the specificity of staphopain A (Leu) from that of both staphopains B and C (Phe/Tyr). However, we show that at the same time the overall specificity of staphopains is relaxed, insofar as multiple substrates that diverge from the sequences described above are also efficiently hydrolyzed.
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Affiliation(s)
- Magdalena Kalińska
- Department of Microbiology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
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Jabaiah A, Daugherty PS. Directed evolution of protease beacons that enable sensitive detection of endogenous MT1-MMP activity in tumor cell lines. ACTA ACUST UNITED AC 2011; 18:392-401. [PMID: 21439484 DOI: 10.1016/j.chembiol.2010.12.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Revised: 11/24/2010] [Accepted: 12/10/2010] [Indexed: 01/26/2023]
Abstract
Directed evolution was applied to identify peptide substrates with enhanced hydrolysis rates by MT1-MMP suitable for protease beacon development. Screening of a random pentapeptide library, using two-color CLiPS, yielded several substrates identical to motifs in distinct collagens that shared the consensus sequence P-x-G↓L. To identify substrates with enhanced cleavage rates, a second-generation decapeptide library incorporating the consensus was screened under stringent conditions, which resulted in a MxPLG↓(M)/(L)M(G)/(A)R consensus motif. These substrates are hydrolyzed by human-MT1-MMP up to six times faster than reported peptide substrates and are stable in plasma. Finally, incubation of soluble protease beacons incorporating the optimized substrates, but not previous substrates, enabled direct detection of endogenous MT1-MMP activity of human-fibrosarcoma (HT-1080) cells. Extended substrate libraries coupled with CLiPS should be useful to generate more effective activity probes for a variety of proteolytic enzymes.
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Affiliation(s)
- Abeer Jabaiah
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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Xiao Y, Dane KY, Uzawa T, Csordas A, Qian J, Soh HT, Daugherty PS, Lagally ET, Heeger AJ, Plaxco KW. Detection of telomerase activity in high concentration of cell lysates using primer-modified gold nanoparticles. J Am Chem Soc 2011; 132:15299-307. [PMID: 20932008 DOI: 10.1021/ja106513f] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the telomeric repeat amplification protocol (TRAP) has served as a powerful assay for detecting telomerase activity, its use has been significantly limited when performed directly in complex, interferant-laced samples. In this work, we report a modification of the TRAP assay that allows the detection of high-fidelity amplification of telomerase products directly from concentrated cell lysates. Briefly, we covalently attached 12 nm gold nanoparticles (AuNPs) to the telomere strand (TS) primer, which is used as a substrate for telomerase elongation. These TS-modified AuNPs significantly reduce polymerase chain reaction (PCR) artifacts (such as primer dimers) and improve the yield of amplified telomerase products relative to the traditional TRAP assay when amplification is performed in concentrated cell lysates. Specifically, because the TS-modified AuNPs eliminate most of the primer-dimer artifacts normally visible at the same position as the shortest amplified telomerase PCR product apparent on agarose gels, the AuNP-modified TRAP assay exhibits excellent sensitivity. Consequently, we observed a 10-fold increase in sensitivity for cancer cells diluted 1000-fold with somatic cells. It thus appears that the use of AuNP-modified primers significantly improves the sensitivity and specificity of the traditional TRAP assay and may be an effective method by which PCR can be performed directly in concentrated cell lysates.
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Affiliation(s)
- Yi Xiao
- Department of Physics, Materials Department, and Institute for Polymers and Organic Solids, University of California, Santa Barbara, California 93106, United States
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Little LE, Dane KY, Daugherty PS, Healy KE, Schaffer DV. Exploiting bacterial peptide display technology to engineer biomaterials for neural stem cell culture. Biomaterials 2010; 32:1484-94. [PMID: 21129772 DOI: 10.1016/j.biomaterials.2010.10.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 10/15/2010] [Indexed: 12/16/2022]
Abstract
Stem cells are often cultured on substrates that present extracellular matrix (ECM) proteins; however, the heterogeneous and poorly defined nature of ECM proteins presents challenges both for basic biological investigation of cell-matrix investigations and translational applications of stem cells. Therefore, fully synthetic, defined materials conjugated with bioactive ligands, such as adhesive peptides, are preferable for stem cell biology and engineering. However, identifying novel ligands that engage cellular receptors can be challenging, and we have thus developed a high throughput approach to identify new adhesive ligands. We selected an unbiased bacterial peptide display library for the ability to bind adult neural stem cells (NSCs), and 44 bacterial clones expressing peptides were identified and found to bind to NSCs with high avidity. Of these clones, four contained RGD motifs commonly found in integrin binding domains, and three exhibited homology to ECM proteins. Three peptide clones were chosen for further analysis, and their synthetic analogs were adsorbed on tissue culture polystyrene (TCPS) or grafted onto an interpenetrating polymer network (IPN) for cell culture. These three peptides were found to support neural stem cell self-renewal in defined medium as well as multi-lineage differentiation. Therefore, bacterial peptide display offers unique advantages to isolate bioactive peptides from large, unbiased libraries for applications in biomaterials engineering.
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Affiliation(s)
- Lauren E Little
- Department of Chemical Engineering, University of California at Berkeley, Berkeley, CA 94720, United States
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35
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Boulware KT, Jabaiah A, Daugherty PS. Evolutionary optimization of peptide substrates for proteases that exhibit rapid hydrolysis kinetics. Biotechnol Bioeng 2010; 106:339-46. [PMID: 20148412 DOI: 10.1002/bit.22693] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protease cleavage site recognition motifs can be identified using protease substrate discovery methodologies, but typically exhibit non-optimal specificity and activity. To enable evolutionary optimization of substrate cleavage kinetics, a two-color cellular library of peptide substrates (CLiPS) methodology was developed. Two-color CLiPS was applied to identify peptide substrates for the tobacco etch virus (TEV) protease from a random pentapeptide library, which were then optimized by screening of a focused, extended substrate library. Quantitative library screening yielded seven amino acid substrates exhibiting rapid hydrolysis by TEV protease and high sequence similarity to the native seven-amino-acid substrate, with a strong consensus of EXLYPhiQG. Comparison of hydrolysis rates for a family of closely related substrates indicates that the native seven-residue TEV substrate co-evolved with TEV protease to facilitate highly efficient hydrolysis. Consensus motifs revealed by screening enabled database identification of a family of related, putative viral protease substrates. More generally, our results suggest that substrate evolution using CLiPS may be useful for optimizing substrate selectivity and activity to enable the design of more effective protease activity probes, molecular imaging agents, and prodrugs.
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Affiliation(s)
- Kevin T Boulware
- Department of Chemical Engineering, University of California-Santa Barbara, 93106, USA
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36
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Karim AY, Kulczycka M, Kantyka T, Dubin G, Jabaiah A, Daugherty PS, Thogersen IB, Enghild JJ, Nguyen KA, Potempa J. A novel matrix metalloprotease-like enzyme (karilysin) of the periodontal pathogen Tannerella forsythia ATCC 43037. Biol Chem 2010; 391:105-17. [PMID: 19919176 DOI: 10.1515/bc.2010.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteases of Tannerella forsythia, a pathogen associated with periodontal disease, are implicated as virulence factors. Here, we characterized a matrix metalloprotease (MMP)-like enzyme of T. forsythia referred to as karilysin. Full-length (without a signal peptide) recombinant karilysin (49.9 kDa) processed itself into the mature 18-kDa enzyme through sequential autoproteolytic cleavage at both N- and C-terminal profragments. The first cleavage at the Asn14-Tyr15 peptide bond generated the fully active enzyme (47.9 kDa) and subsequent truncations at the C-terminus did not affect proteolytic activity. Mutation of Tyr15 to Ala generated a prokarilysin variant that processed itself into the final 18-kDa form with greatly reduced kinetics. Inactive prokarilysin with the mutated catalytic Glu residue (E136A) was processed by active karilysin at the same sites as the active enzymes. Karilysin proteolytic activity and autoprocessing were inhibited by 1,10-phenanthroline and EDTA. Calcium ions were found to be important for both the activity and thermal stability of karilysin. Using CLiPS technology, the specificity of karilysin was found to be similar to that of MMPs with preference for Leu/Tyr/Met at P1' and Pro/Ala at P3. This specificity and the ability to degrade elastin, fibrinogen and fibronectin may contribute to the pathogenicity of periodontitis.
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Affiliation(s)
- Abdulkarim Y Karim
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
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37
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Abstract
A quantitative screening method was developed to enable isolation and affinity maturation of peptide ligands specific for a given target from peptide libraries displayed on the outer surface of Escherichia coli using multi-parameter flow cytometry. From a large, random 15-mer peptide library, screening identified a core motif of W-E/D-W-E/D that conferred binding to vascular endothelial growth factor (VEGF). One cycle of affinity maturation resulted in the identification of several families of VEGF-binding peptides having distinct consensus sequences, from which a preferred disulfide constraint emerged. In the second affinity maturation cycle, high affinity peptides were favored by the addition of a decoy protein that bound an adjacent epitope on the display scaffold. The decoy apparently reduced rebinding or avidity effects, and the resulting peptides exhibited consensus at 12 of 19 amino acid positions. Peptides identified and affinity matured using bacterial display were remarkably similar to the best affinity matured using phage display and exhibited comparable dissociation constants (within 2-fold; K(D) = 4.7 x 10(-7) M). Screening of bacterial-displayed peptide libraries using cytometry enabled optimization of screening conditions to favor affinity and specificity and rapid clonal characterization. Bacterial display thus provides a new quantitative tool for the discovery and evolutionary optimization of protein-specific peptide ligands.
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Affiliation(s)
- Sophia A Kenrick
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
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38
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Abstract
A general method was developed for the discovery of protease-activated binding ligands, or proligands, from combinatorial prodomain libraries displayed on the surface of E. coli. Peptide libraries of candidate prodomains were fused with a matrix metalloprotease-2 substrate linker to a vascular endothelial growth factor-binding peptide and sorted using a two-stage flow cytometry screening procedure to isolate proligands that required protease treatment for binding activity. Prodomains that imparted protease-mediated switching activity were identified after three sorting cycles using two unique library design strategies. The best performing proligand exhibited a 100-fold improvement in apparent binding affinity after exposure to protease. This method may prove useful for developing therapeutic and diagnostic ligands with improved systemic targeting specificity.
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Affiliation(s)
- Jerry M Thomas
- Department of Chemical Engineering, University of California, Santa Barbara, 93106, USA
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39
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Hall SS, Daugherty PS. Quantitative specificity-based display library screening identifies determinants of antibody-epitope binding specificity. Protein Sci 2009; 18:1926-34. [PMID: 19610073 DOI: 10.1002/pro.203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Despite the critical importance of molecular specificity in bimolecular systems, in vitro display technologies have been applied extensively for affinity maturation of peptides and antibodies without explicitly measuring the specificity of the desired interaction. We devised a general strategy to measure, screen, and evolve specificity of protein ligand interactions analogous to widely used affinity maturation strategies. The specificity of binding to target and nontarget antibodies labeled with spectrally distinct fluorophores was measured simultaneously in protein mixtures via multiparameter flow cytometry, thereby enabling screening for high target antibody specificity. Isolated antibody specific ligands exhibited varying specificity, revealing critical amino acid determinants for target recognition and nontarget avoidance in complex mixtures. Molecular specificity in the mixture was further enhanced by quantitative directed evolution, yielding a family of epitopes exhibiting improved specificities equivalent, or superior to, the native peptide antigen to which the antibody was raised. Specificity screening simultaneously favored affinity, yielding ligands with three-fold improved affinity relative to the parent epitope. Quantitative specificity screening will be useful to screen, evolve, and characterize the specificity of protein and peptide interactions for molecular recognition applications.
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Affiliation(s)
- Sejal S Hall
- The Institute for Energy Efficiency, University of California, Santa Barbara, California 93106, USA
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40
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Abstract
Cancer heterogeneity renders risk stratification and therapy decisions challenging. Thus, genomic and proteomic methodologies have been used in an effort to identify biomarkers that can differentiate tumor subtypes to improve therapeutic outcome. Here, we report a generally applicable strategy to generate tumor type-specific peptide ligand arrays. Peptides that specifically recognize breast tumor-derived cell lines (MDA-MB-231, MCF-7, and T47-D) were identified using cell-displayed peptide libraries carrying an intrinsic fluorescent marker allowing for sorting and characterization with quantitative flow cytometry. Tumor cell specificity was achieved by depleting libraries of ligands binding to normal mammary epithelial cells (HMEC and MCF-10A). Although integrin binding RGD motifs were favored by some cell lines, screening with RGD competitors yielded several novel consensus motifs exhibiting improved tumor specificity. The resultant peptide array contained multiple consensus motifs exhibiting strong similarity to breast tumor-associated proteins. Profiling a panel of breast cancer cell lines with the peptide array revealed receptor expression patterns distinctive for luminal or basal tumor subtypes. In addition, peptide displaying bacteria and peptide functionalized microparticles enabled fluorescent labeling of tumor cells and frozen tumor tissue sections. Our results indicate that cell surface profiling using highly specific breast tumor cell binding ligands may provide an efficient route for tumor subtype classification, biomarker identification, and for the development of targeted diagnostics and therapeutics.
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Affiliation(s)
- Karen Y Dane
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, USA
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41
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Abstract
The ability to rapidly and efficiently isolate specific viruses, bacteria, or mammalian cells from complex mixtures lies at the heart of biomedical applications ranging from in vitro diagnostics to cell transplantation therapies. Unfortunately, many current selection methods for cell separation, such as magnetic activated cell sorting (MACS), only allow the binary separation of target cells that have been labeled via a single parameter (e.g., magnetization). This limitation makes it challenging to simultaneously enrich multiple, distinct target cell types from a multicomponent sample. We describe here a novel approach to specifically label multiple cell types with unique synthetic dielectrophoretic tags that modulate the complex permittivities of the labeled cells, allowing them to be sorted with high purity using the multitarget dielectrophoresis activated cell sorter (MT-DACS) chip. Here we describe the underlying physics and design of the MT-DACS microfluidic device and demonstrate approximately 1000-fold enrichment of multiple bacterial target cell types in a single-pass separation.
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Affiliation(s)
- Unyoung Kim
- Department of Mechanical Engineering, University of California, Santa Barbara, California 93106, USA
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42
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Abstract
Bacterial cell-surface display systems coupled with quantitative screening methods offer the potential to expand protein engineering capabilities. To more fully exploit this potential, a unique bacterial surface display scaffold was engineered to display peptides more efficiently from the surface exposed C- and N-termini of a circularly permuted outer membrane protein. Using directed evolution, efficient membrane localization of a circularly permuted OmpX (CPX) display scaffold was rescued, thereby improving the presentation of diverse passenger peptides on the cell surface. Random and targeted mutagenesis directed towards linkers joining the native N- and C-termini of OmpX coupled with screening by FACS yielded an enhanced CPX (eCPX) variant which localized to the outer membrane as efficiently as the non-permuted parent. Interestingly, enhancing substitutions coincided with a C-terminal motif conserved in outer membrane proteins. Surface localization of various passenger peptides and mini-proteins was expedited using eCPX relative to that achieved with the parent scaffold. The new variant also permitted simultaneous display and labeling of distinct peptides on structurally adjacent C- and N-termini, thus enabling display level normalization during library screening and the display of bidentate or dimeric peptides. Consequently, the evolved scaffold, eCPX, expands the range of applications for bacterial display. Finally, this approach provides a route to improve the performance of cell-surface display vectors for protein engineering and design.
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Affiliation(s)
- Jeffrey J Rice
- Department of Chemical Engineering, Institute of Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106, USA
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43
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Dubin G, Stec-Niemczyk J, Kisielewska M, Pustelny K, Popowicz GM, Bista M, Kantyka T, Boulware KT, Stennicke HR, Czarna A, Phopaisarn M, Daugherty PS, Thøgersen IB, Enghild JJ, Thornberry N, Dubin A, Potempa J. Enzymatic activity of the Staphylococcus aureus SplB serine protease is induced by substrates containing the sequence Trp-Glu-Leu-Gln. J Mol Biol 2008; 379:343-56. [PMID: 18448121 DOI: 10.1016/j.jmb.2008.03.059] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 03/21/2008] [Accepted: 03/25/2008] [Indexed: 12/18/2022]
Abstract
Proteases are of significant importance for the virulence of Staphylococcus aureus. Nevertheless, their subset, the serine protease-like proteins, remains poorly characterized. Here presented is an investigation of SplB protease catalytic activity revealing that the enzyme possesses exquisite specificity and only cleaves efficiently after the sequence Trp-Glu-Leu-Gln. To understand the molecular basis for such selectivity, we solved the three-dimensional structure of SplB to 1.8 A. Modeling of substrate binding to the protease demonstrated that selectivity relies in part on a canonical specificity pockets-based mechanism. Significantly, the conformation of residues that ordinarily form the oxyanion hole, an essential structural element of the catalytic machinery of serine proteases, is not canonical in the SplB structure. We postulate that within SplB, the oxyanion hole is only formed upon docking of a substrate containing the consensus sequence motif. It is suggested that this unusual activation mechanism is used in parallel with classical determinants to further limit enzyme specificity. Finally, to guide future development, we attempt to point at likely physiological substrates and thus the role of SplB in staphylococcal physiology.
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Affiliation(s)
- Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
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44
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Abstract
Recent improvements in bacterial surface display systems coupled with efficient selection and screening strategies are propelling bacterial display systems to the forefront of peptide and protein engineering. The ability to analyze and screen very large protein libraries using cell-sorting instrumentation coupled with the ease of manipulating bacteria provides new capabilities for the protein engineering toolbox.
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Affiliation(s)
- Patrick S Daugherty
- Department of Chemical Engineering, Biomolecular Science and Engineering, and Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106, USA.
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45
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Abstract
Peptide ligands capable of mediating nanoparticle adhesion to human red blood cells (RBCs) were identified from a large bacterial display peptide library. Peptides were displayed on the surface of fluorescent Escherichia coli, enabling quantitative measurement of RBC binding and high-throughput screening using fluorescence-activated cell sorting. One of the isolated clones remained attached to RBCs under high-shear stresses equivalent to those encountered in vivo. Furthermore, nanoparticles functionalized with the identified RBC-binding peptides exhibited nearly 100-fold increased RBC binding relative to nonfunctionalized particles in the presence of physiologically relevant concentrations of human serum albumin, indicating that peptides remained functional in the absence of the protein scaffold used for display. The RBC-binding peptides identified here provide new opportunities for sustained therapeutic delivery applications whereby nanoparticulate drug carriers can be attached to RBCs to achieve long-circulating carrier systems.
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Affiliation(s)
- Sejal S Hall
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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46
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Abstract
The capability to screen molecular libraries using disposable microfluidic devices provides the potential to simplify and automate reagent generation and to develop integrated bioanalytical systems for clinical diagnostics. Here, antibody epitopes were mapped using a disposable microfluidic device to screen a combinatorial peptide library composed of 5 x 108 members displayed on bacterial cells. On-chip library screening was achieved in a two-stage, continuous-flow microfluidic sorter that separates antibody-binding target cells captured on microspheres through dielectrophoretic funneling. The antibody fingerprints identified were comparable to those obtained using state-of-the-art commercial cell sorting instrumentation.
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Affiliation(s)
- Paul H Bessette
- Department of Chemical Engineering, and Institute for Collaborative Biotechnologies, University of California, Santa Barbara, California 93106, USA
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47
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Abstract
Protein microarray technology, in which a large number of capture ligands are spatially arrayed at a high density, presents an attractive method for high-throughput proteomic analysis. Toward this end, we demonstrate the first cell-based protein detection in a microsystem, wherein Escherichia coli cells are genetically engineered to express the desired capture proteins on the membrane surface and are spatially arrayed as sensing elements in a microfluidic device. An E. coli clone expressing peptide ligands with high affinity and high specificity for target molecules was isolated a priori. Then these cells were electrokinetically immobilized on gold electrodes using dielectrophoresis, thus allowing each sensor element to be electrically addressable. Flow cytometry and subsequent fluorescence analysis verified the highly specific capture and detection of target molecules by the bacteria. Finally, through the coexpression of peptide-based capture ligands on the cell surface and fluorescent protein in the cytoplasm, we demonstrate an effective means of directly linking the fluorescence intensity to the density of capture ligands.
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Affiliation(s)
- Sang-Hyun Oh
- California Nanosystems Institute and Biomolecular Science and Engineering Program, University of California-Santa Barbara, California 93106, USA
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48
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Abstract
A quantitative methodology was developed to identify protein interactions in a broad range of cell types by using FRET between fluorescent proteins. Genetic fusions of a target receptor to a FRET acceptor and a large library of candidate peptide ligands to a FRET donor enabled high-throughput optical screening for optimal interaction partners in the cytoplasm of Escherichia coli. Flow cytometric screening identified a panel of peptide ligands capable of recognizing the target receptors in the intracellular environment. For both SH3 and PDZ domain-type target receptors, physiologically meaningful consensus sequences were apparent among the isolated ligands. The relative dissociation constants of interacting partners could be measured directly by using a dilution series of cell lysates containing FRET hybrids, providing a previously undescribed high-throughput approach to rank the affinity of many interaction partners. FRET hybrid interaction screening provides a powerful tool to discover protein ligands in the cellular context with potential applications to a wide variety of eukaryotic cell types.
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Affiliation(s)
- Xia You
- *Department of Chemical Engineering, University of California, Santa Barbara, CA 93106; and
| | - Annalee W. Nguyen
- *Department of Chemical Engineering, University of California, Santa Barbara, CA 93106; and
| | - Abeer Jabaiah
- *Department of Chemical Engineering, University of California, Santa Barbara, CA 93106; and
| | - Mark A. Sheff
- Bauer Center for Genomics Research, Room 208, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138
| | - Kurt S. Thorn
- Bauer Center for Genomics Research, Room 208, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138
| | - Patrick S. Daugherty
- *Department of Chemical Engineering, University of California, Santa Barbara, CA 93106; and
- To whom correspondence should be addressed. E-mail:
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49
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Mena MA, Treynor TP, Mayo SL, Daugherty PS. Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library. Nat Biotechnol 2006; 24:1569-71. [PMID: 17115054 DOI: 10.1038/nbt1264] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 10/11/2006] [Indexed: 11/09/2022]
Abstract
The utility of blue fluorescent protein (BFP) has been limited by its low quantum yield and rapid photobleaching. A library targeting residues neighboring the chromophore yielded a variant with enhanced quantum yield (0.55 versus 0.34), reduced pH sensitivity and a 40-fold increase in photobleaching half-life. This BFP, named Azurite, is well expressed in bacterial and mammalian cells and extends the palette of fluorescent proteins that can be used for imaging.
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Affiliation(s)
- Marco A Mena
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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50
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Rice JJ, Schohn A, Bessette PH, Boulware KT, Daugherty PS. Bacterial display using circularly permuted outer membrane protein OmpX yields high affinity peptide ligands. Protein Sci 2006; 15:825-36. [PMID: 16600968 PMCID: PMC2242469 DOI: 10.1110/ps.051897806] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A bacterial display methodology was developed for N- and C-terminal display and demonstrated to enable rapid screening of very large peptide libraries with high precision and efficiency. To overcome limitations of insertional fusion display libraries, a new scaffold was developed through circular permutation of the Escherichia coli outer membrane protein OmpX that presents both N and C termini on the external cell surface. Circularly permuted OmpX (CPX) display was directly compared to insertional fusion display by screening comparable peptide libraries in each format using magnetic and fluorescence activated cell sorting. CPX display enabled in situ measurement of dissociation rate constants with improved accuracy and, consequently, improved affinity discrimination during screening and ranking of isolated clones. Using streptavidin as a model target, bacterial display yielded the well-characterized HP(Q)/(M) motif obtained previously using several alternative peptide display systems, as well as three additional motifs (L(I)/(V) CQNVCY, CGWMY(F)/(Y)xEC, ERCWYVMHWPCNA). Using CPX display, a very high affinity streptavidin-binding peptide was isolated having a dissociation rate constant k(off) = 0.002sec(-1) even after grafting to the C terminus of an unrelated protein. Comparison of individual clones obtained from insertional fusion and terminal fusion libraries suggests that the N-terminal display yields sequences with greater diversity, affinity, and modularity. CPX bacterial display thus provides a highly effective method for screening peptide libraries to rapidly generate ligands with high affinity and specificity.
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Affiliation(s)
- Jeffrey J Rice
- Department of Chemical Engineering, University of California, Santa Brabara, 93106, USA
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