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Tiu CK, Zhu F, Wang LF, de Alwis R. Phage ImmunoPrecipitation Sequencing (PhIP-Seq): The Promise of High Throughput Serology. Pathogens 2022; 11:pathogens11050568. [PMID: 35631089 PMCID: PMC9143919 DOI: 10.3390/pathogens11050568] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Determining the exposure or infection history of a person to a multitude of viruses is not an easy task. Typically, antibody tests detect antibodies against proteins (antigens) to only one or a few viruses. Here, we review an emerging technology called Phage ImmunoPrecipitation Sequencing (PhIP-Seq), that allows us to study the infection history of individuals to large numbers of viruses simultaneously. This technology uses bacteriophages to express and display viral antigens of choice, which are then bound by antigen-specific antibodies in patient samples. Antibody-bound bacteriophages are pulled down and identified through molecular techniques. This technology has been used in various infectious disease scenarios, including assessing exposure to different viruses, studying vaccine responses, and identifying viral cause of diseases. Despite inherent limitations in presenting only peptides, this technology holds great promise for future application in identifying novel pathogens, one health and pandemic preparedness. Abstract Phage ImmunoPrecipitation Sequencing (PhIP-Seq) is a high throughput serological technology that is revolutionizing the manner in which we track antibody profiles. In this review, we mainly focus on its application to viral infectious diseases. Through the pull-down of patient antibodies using peptide-tile-expressing T7 bacteriophages and detection using next-generation sequencing (NGS), PhIP-Seq allows the determination of antibody repertoires against peptide targets from hundreds of proteins and pathogens. It differs from conventional serological techniques in that PhIP-Seq does not require protein expression and purification. It also allows for the testing of many samples against the whole virome. PhIP-Seq has been successfully applied in many infectious disease investigations concerning seroprevalence, risk factors, time trends, etiology of disease, vaccinology, and emerging pathogens. Despite the inherent limitations of this technology, we foresee the future expansion of PhIP-Seq in both investigative studies and tracking of current, emerging, and novel viruses. Following the review of PhIP-Seq technology, its limitations, and applications, we recommend that PhIP-Seq be integrated into national surveillance programs and be used in conjunction with molecular techniques to support both One Health and pandemic preparedness efforts.
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Affiliation(s)
- Charles Kevin Tiu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- SingHealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- SingHealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Ruklanthi de Alwis
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- Viral Research and Experimental Medicine Centre (ViREMiCS), SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore
- Correspondence:
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Wang JY, Roehrl MW, Roehrl VB, Roehrl MH. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.07.30.454526. [PMID: 34373855 PMCID: PMC8351778 DOI: 10.1101/2021.07.30.454526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. The autoantigen-ome is significantly associated with various processes in viral infections, such as translation, protein processing, and vesicle transport. Interestingly, the coding genes of autoAgs predominantly contain multiple exons with many possible alternative splicing variants, short transcripts, and short UTR lengths. These observations and the finding that numerous autoAgs involved in RNA-splicing showed altered expression in viral infections suggest that viruses exploit alternative splicing to reprogram host cell machinery to ensure viral replication and survival. While each cell type gives rise to a unique pool of autoAgs, 39 common autoAgs associated with cell stress and apoptosis were identified from all six cell types, with several being known markers of systemic autoimmune diseases. In particular, the common autoAg UBA1 that catalyzes the first step in ubiquitination is encoded by an X-chromosome escape gene. Given its essential function in apoptotic cell clearance and that X-inactivation escape tends to increase with aging, UBA1 dysfunction can therefore predispose aging women to autoimmune disorders. In summary, we propose a model of how viral infections lead to extensive molecular alterations and host cell death, autoimmune responses facilitated by autoAg-DS complexes, and ultimately autoimmune diseases. Overall, this master autoantigen-ome provides a molecular guide for investigating the myriad of autoimmune sequalae to COVID-19 and clues to the rare but reported adverse effects of the currently available COVID vaccines.
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Affiliation(s)
| | | | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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Tang F, LeBlanc ME, Wang W, Liang D, Chen P, Chou TH, Tian H, Li W. Anti-secretogranin III therapy of oxygen-induced retinopathy with optimal safety. Angiogenesis 2019; 22:369-382. [PMID: 30644010 DOI: 10.1007/s10456-019-09662-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/07/2019] [Indexed: 12/17/2022]
Abstract
Retinopathy of prematurity (ROP) with pathological retinal neovascularization is the most common cause of blindness in children. ROP is currently treated with laser therapy or cryotherapy, both of which may adversely affect the peripheral vision with limited efficacy. Owing to the susceptibility of the developing retina and vasculatures to pharmacological intervention, there is currently no approved drug therapy for ROP in preterm infants. Secretogranin III (Scg3) was recently discovered as a highly disease-restricted angiogenic factor, and a Scg3-neutralizing monoclonal antibody (mAb) was reported with high efficacy to alleviate oxygen-induced retinopathy (OIR) in mice, a surrogate model of ROP. Herein we independently investigated the efficacy of anti-Scg3 mAb in OIR mice and characterized its safety in neonatal mice. We developed a new Scg3-neutralizing mAb recognizing a distinct epitope and independently established the therapeutic activity of anti-Scg3 therapy to alleviate OIR-induced pathological retinal neovascularization in mice. Importantly, anti-Scg3 mAb showed no detectable adverse effects on electroretinography and developing retinal vasculature. Furthermore, systemic anti-Scg3 mAb induced no renal tubular injury or abnormality in kidney vessel development and body weight gain of neonatal mice. In contrast, anti-vascular endothelial growth factor drug aflibercept showed significant side effects in neonatal mice. These results suggest that anti-Scg3 mAb may have the safety and efficacy profiles required for ROP therapy.
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Affiliation(s)
- Fen Tang
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Michelle E LeBlanc
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Weiwen Wang
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Dan Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Ping Chen
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
- Department of Ophthalmology, Renji Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Tsung-Han Chou
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Hong Tian
- Everglades Biopharma, LLC, Miami, FL, USA
| | - Wei Li
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA.
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4
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Lee JM, Kim JY, Bok J, Kim KS, Choi JY, Kim SH. Identification of evidence for autoimmune pathology of bilateral sudden sensorineural hearing loss using proteomic analysis. Clin Immunol 2017. [DOI: 10.1016/j.clim.2017.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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5
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LeBlanc ME, Wang W, Chen X, Caberoy NB, Guo F, Shen C, Ji Y, Tian H, Wang H, Chen R, Li W. Secretogranin III as a disease-associated ligand for antiangiogenic therapy of diabetic retinopathy. J Exp Med 2017; 214:1029-1047. [PMID: 28330905 PMCID: PMC5379984 DOI: 10.1084/jem.20161802] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/23/2016] [Accepted: 02/15/2017] [Indexed: 12/20/2022] Open
Abstract
LeBlanc et al. uncover secretogranin III (Scg3) as a unique disease-associated vascular permeability and angiogenic factor using comparative ligandomics. Scg3-neutralizing antibodies alleviate vascular leakage in diabetic retinopathy mice and retinal neovascularization in oxygen-induced retinopathy mice with high efficacy. Diabetic retinopathy (DR) is a leading cause of vision loss with retinal vascular leakage and/or neovascularization. Current antiangiogenic therapy against vascular endothelial growth factor (VEGF) has limited efficacy. In this study, we applied a new technology of comparative ligandomics to diabetic and control mice for the differential mapping of disease-related endothelial ligands. Secretogranin III (Scg3) was discovered as a novel disease-associated ligand with selective binding and angiogenic activity in diabetic but not healthy vessels. In contrast, VEGF bound to and induced angiogenesis in both diabetic and normal vasculature. Scg3 and VEGF signal through distinct receptor pathways. Importantly, Scg3-neutralizing antibodies alleviated retinal vascular leakage in diabetic mice with high efficacy. Furthermore, anti-Scg3 prevented retinal neovascularization in oxygen-induced retinopathy mice, a surrogate model for retinopathy of prematurity (ROP). ROP is the most common cause of vision impairment in children, with no approved drug therapy. These results suggest that Scg3 is a promising target for novel antiangiogenic therapy of DR and ROP.
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Affiliation(s)
- Michelle E LeBlanc
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136
| | - Weiwen Wang
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136
| | - Xiuping Chen
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136.,Department of Ophthalmology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Nora B Caberoy
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154
| | - Feiye Guo
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136
| | - Chen Shen
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136
| | - Yanli Ji
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136.,Department of Ophthalmology, Zhengzhou Eye Hospital, Zhengzhou 450000, Henan, China
| | - Hong Tian
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136.,School of Public Health, Xinxiang Medical University, Xinxiang, Henan 453003, China.,Everglades Biopharma, Miami, FL 33156
| | - Hui Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Wei Li
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136 .,Vascular Biology Institute, University of Miami School of Medicine, Miami, FL 33136
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Guo F, Ding Y, Caberoy N, Alvarado G, Wang F, Chen R, Li W. ABCF1 extrinsically regulates retinal pigment epithelial cell phagocytosis. Mol Biol Cell 2015; 26:2311-20. [PMID: 25904329 PMCID: PMC4462947 DOI: 10.1091/mbc.e14-09-1343] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 04/14/2015] [Indexed: 12/24/2022] Open
Abstract
Intracellular ABCF1 is identified and characterized as a new ligand to extrinsically stimulate retinal pigment epithelial cell phagocytosis. A new approach developed in this study is broadly applicable to many other phagocytes and will enable systematic elucidation of their ligands to broaden understanding of extrinsic regulation and cargo recognition. Phagocytosis of shed photoreceptor outer segments (POSs) by retinal pigment epithelial (RPE) cells is critical to retinal homeostasis and shares many conserved signaling pathways with other phagocytes, including extrinsic regulations. Phagocytotic ligands are the key to cargo recognition, engulfment initiation, and activity regulation. In this study, we identified intracellular protein ATP-binding cassette subfamily F member 1 (ABCF1) as a novel RPE phagocytotic ligand by a new approach of functional screening. ABCF1 was independently verified to extrinsically promote phagocytosis of shed POSs by D407 RPE cells. This finding was further corroborated with primary RPE cells and RPE explants. Internalized POS vesicles were colocalized with a phagosome marker, suggesting that ABCF1-mediated engulfment is through a phagocytic pathway. ABCF1 was released from apoptotic cells and selectively bound to shed POS vesicles and apoptotic cells, possibly via externalized phosphatidylserine. ABCF1 is predominantly expressed in POSs and colocalized with the POS marker rhodopsin, providing geographical convenience for regulation of RPE phagocytosis. Collectively these results suggest that ABCF1 is released from and binds to shed POSs in an autocrine manner to facilitate RPE phagocytosis through a conserved pathway. Furthermore, the new approach is broadly applicable to many other phagocytes and will enable systematic elucidation of their ligands to understand extrinsic regulation and cargo recognition.
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Affiliation(s)
- Feiye Guo
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, FL 33136
| | - Ying Ding
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, FL 33136
| | - Nora Caberoy
- School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, NV 89154
| | - Gabriela Alvarado
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, FL 33136
| | - Feng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
| | - Wei Li
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, FL 33136
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Guo F, Ding Y, Caberoy NB, Alvarado G, Liu R, Shen C, Yu J, Zhou Y, Salero E, LeBlanc ME, Wang W, Li W. Lyar Is a New Ligand for Retinal Pigment Epithelial Phagocytosis. J Cell Biochem 2015; 116:2177-87. [PMID: 25735755 DOI: 10.1002/jcb.25089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/18/2014] [Accepted: 01/16/2015] [Indexed: 01/12/2023]
Abstract
Phagocytosis is critical to tissue homeostasis, as highlighted by phagocytosis defect of retinal pigment epithelial (RPE) cells with debris accumulation, photoreceptor degeneration and blindness. Phagocytosis ligands are the key to delineating molecular mechanisms and functional roles of phagocytes, but are traditionally identified in individual cases with technical challenges. We recently developed open reading frame phage display (OPD) for phagocytosis-based functional cloning (PFC) to identify unknown ligands. One of the identified ligands was Ly-1 antibody reactive clone (Lyar) with functions poorly defined. Herein, we characterized Lyar as a new ligand to stimulate RPE phagocytosis. In contrast to its reported nucleolar expression, immunohistochemistry showed that Lyar was highly expressed in photoreceptor outer segments (POSs) of the retina. Cytoplasmic Lyar was released from apoptotic cells, and selectively bound to shed POSs and apoptotic cells, but not healthy cells. POS vesicles engulfed through Lyar-dependent pathway were targeted to phagosomes and colocalized with phagosome marker Rab7. These results suggest that Lyar is a genuine RPE phagocytosis ligand, which in turn supports the validity of OPD/PFC as the only available approach for unbiased identification of phagocytosis ligands with broad applicability to various phagocytes.
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Affiliation(s)
- Feiye Guo
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Ying Ding
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Nora B Caberoy
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, 89154
| | - Gabriela Alvarado
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Robert Liu
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Chen Shen
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Jisu Yu
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Yixiong Zhou
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 200011, Shanghai, China
| | - Enrique Salero
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Michelle E LeBlanc
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Weiwen Wang
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
| | - Wei Li
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida, 33136
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Interaction analysis through proteomic phage display. BIOMED RESEARCH INTERNATIONAL 2014; 2014:176172. [PMID: 25295249 PMCID: PMC4177731 DOI: 10.1155/2014/176172] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/11/2014] [Accepted: 08/19/2014] [Indexed: 11/29/2022]
Abstract
Phage display is a powerful technique for profiling specificities of peptide binding domains. The method is suited for the identification of high-affinity ligands with inhibitor potential when using highly diverse combinatorial peptide phage libraries. Such experiments further provide consensus motifs for genome-wide scanning of ligands of potential biological relevance. A complementary but considerably less explored approach is to display expression products of genomic DNA, cDNA, open reading frames (ORFs), or oligonucleotide libraries designed to encode defined regions of a target proteome on phage particles. One of the main applications of such proteomic libraries has been the elucidation of antibody epitopes. This review is focused on the use of proteomic phage display to uncover protein-protein interactions of potential relevance for cellular function. The method is particularly suited for the discovery of interactions between peptide binding domains and their targets. We discuss the largely unexplored potential of this method in the discovery of domain-motif interactions of potential biological relevance.
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Tezel G. A proteomics view of the molecular mechanisms and biomarkers of glaucomatous neurodegeneration. Prog Retin Eye Res 2013; 35:18-43. [PMID: 23396249 DOI: 10.1016/j.preteyeres.2013.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 02/07/2023]
Abstract
Despite improving understanding of glaucoma, key molecular players of neurodegeneration that can be targeted for treatment of glaucoma, or molecular biomarkers that can be useful for clinical testing, remain unclear. Proteomics technology offers a powerful toolbox to accomplish these important goals of the glaucoma research and is increasingly being applied to identify molecular mechanisms and biomarkers of glaucoma. Recent studies of glaucoma using proteomics analysis techniques have resulted in the lists of differentially expressed proteins in human glaucoma and animal models. The global analysis of protein expression in glaucoma has been followed by cell-specific proteome analysis of retinal ganglion cells and astrocytes. The proteomics data have also guided targeted studies to identify post-translational modifications and protein-protein interactions during glaucomatous neurodegeneration. In addition, recent applications of proteomics have provided a number of potential biomarker candidates. Proteomics technology holds great promise to move glaucoma research forward toward new treatment strategies and biomarker discovery. By reviewing the major proteomics approaches and their applications in the field of glaucoma, this article highlights the power of proteomics in translational and clinical research related to glaucoma and also provides a framework for future research to functionally test the importance of specific molecular pathways and validate candidate biomarkers.
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Affiliation(s)
- Gülgün Tezel
- Department of Ophthalmology & Visual Sciences, University of Louisville School of Medicine, Louisville, KY, USA.
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Tezel G, Thornton IL, Tong MG, Luo C, Yang X, Cai J, Powell DW, Soltau JB, Liebmann JM, Ritch R. Immunoproteomic analysis of potential serum biomarker candidates in human glaucoma. Invest Ophthalmol Vis Sci 2012; 53:8222-31. [PMID: 23150628 DOI: 10.1167/iovs.12-10076] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Evidence supporting the immune system involvement in glaucoma includes increased titers of serum antibodies to retina and optic nerve proteins, although their pathogenic importance remains unclear. This study using an antibody-based proteomics approach aimed to identify disease-related antigens as candidate biomarkers of glaucoma. METHODS Serum samples were collected from 111 patients with primary open-angle glaucoma and an age-matched control group of 49 healthy subjects without glaucoma. For high-throughput characterization of antigens, serum IgG was eluted from five randomly selected glaucomatous samples and analyzed by linear ion trap mass spectrometry (LC-MS/MS). Serum titers of selected biomarker candidates were then measured by specific ELISAs in the whole sample pool (including an additional control group of diabetic retinopathy). RESULTS LC-MS/MS analysis of IgG elutes revealed a complex panel of proteins, including those detectable only in glaucomatous samples. Interestingly, many of these antigens corresponded to upregulated retinal proteins previously identified in glaucomatous donors (or that exhibited increased methionine oxidation). Moreover, additional analysis detected a greater immunoreactivity of the patient sera to glaucomatous retinal proteins (or to oxidatively stressed cell culture proteins), thereby suggesting the importance of disease-related protein modifications in autoantibody production/reactivity. As a narrowing-down strategy for selection of initial biomarker candidates, we determined the serum proteins overlapping with the retinal proteins known to be up-regulated in glaucoma. Four of the selected 10 candidates (AIF, cyclic AMP-responsive element binding protein, ephrin type-A receptor, and huntingtin) exhibited higher ELISA titers in the glaucomatous sera. CONCLUSIONS A number of serum proteins identified by this immunoproteomic study of human glaucoma may represent diseased tissue-related antigens and serve as candidate biomarkers of glaucoma.
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Affiliation(s)
- Gülgün Tezel
- Department of Ophthalmology & Visual Sciences, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA.
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Bazan J, Całkosiński I, Gamian A. Phage display--a powerful technique for immunotherapy: 1. Introduction and potential of therapeutic applications. Hum Vaccin Immunother 2012; 8:1817-28. [PMID: 22906939 DOI: 10.4161/hv.21703] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
One of the most effective molecular diversity techniques is phage display. This technology is based on a direct linkage between phage phenotype and its encapsulated genotype, which leads to presentation of molecule libraries on the phage surface. Phage display is utilized in studying protein-ligand interactions, receptor binding sites and in improving or modifying the affinity of proteins for their binding partners. Generating monoclonal antibodies and improving their affinity, cloning antibodies from unstable hybridoma cells and identifying epitopes, mimotopes and functional or accessible sites from antigens are also important advantages of this technology. Techniques originating from phage display have been applied to transfusion medicine, neurological disorders, mapping vascular addresses and tissue homing of peptides. Phages have been applicable to immunization therapies, which may lead to development of new tools used for treating autoimmune and cancer diseases. This review describes the phage display technology and presents the recent advancements in therapeutic applications of phage display.
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Affiliation(s)
- Justyna Bazan
- Department of Medical Biochemistry; Wroclaw Medical University; Wroclaw, Poland.
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12
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Li W. ORF phage display to identify cellular proteins with different functions. Methods 2012; 58:2-9. [PMID: 22836128 DOI: 10.1016/j.ymeth.2012.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 07/11/2012] [Indexed: 01/17/2023] Open
Abstract
Open reading frame (ORF) phage display is a new branch of phage display aimed at improving its efficiency to identify cellular proteins with specific binding or functional activities. Despite the success of phage display with antibody libraries and random peptide libraries, phage display with cDNA libraries of cellular proteins identifies a high percentage of non-ORF clones encoding unnatural short peptides with minimal biological implications. This is mainly because of the uncontrollable reading frames of cellular proteins in conventional cDNA libraries. ORF phage display solves this problem by eliminating non-ORF clones to generate ORF cDNA libraries. Here I summarize the procedures of ORF phage display, discuss the factors influencing its efficiency, present examples of its versatile applications, and highlight evidence of its capability of identifying biologically relevant cellular proteins. ORF phage display coupled with different selection strategies is capable of delineating diverse functions of cellular proteins with unique advantages.
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Affiliation(s)
- Wei Li
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA.
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Abstract
Autoimmune uveitis (AIU) is among the leading causes of preventable blindness. It can be isolated, precede, or appear in the course of a systemic autoimmune inflammatory disease. When suspected, AIU should be promptly referred to an ophthalmologist for proper anatomic classification and local treatment. In recurrent and chronic forms, systemic treatment should be started, usually with corticosteroids and immunesuppressors. In cases of lack of efficacy or intolerance, biologic agents such as monoclonal antibodies anti-TNF (infliximab and adalimumab) and others (abatacept and tocilizumab) are being used. The clinical diseases associated to AIU and the experimental models have helped in the understanding of the pathogenic mechanism. The treatment schemes have improved, and recent advances in basic knowledge are leading to even more effective targeted therapies.
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Caberoy NB, Alvarado G, Bigcas JL, Li W. Galectin-3 is a new MerTK-specific eat-me signal. J Cell Physiol 2012; 227:401-7. [PMID: 21792939 DOI: 10.1002/jcp.22955] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phagocytosis of apoptotic cells and cellular debris is a critical process of maintaining tissue and immune homeostasis. Defects in the phagocytosis process cause autoimmunity and degenerative diseases. Phagocytosis ligands or "eat-me" signals control the initiation of the process by linking apoptotic cells to receptors on phagocyte surface and triggering signaling cascades for cargo engulfment. Eat-me signals are traditionally identified on a case-by-case basis with challenges, and the identification of their cognate receptors is equally daunting. Here, we identified galectin-3 (Gal-3) as a new MerTK ligand by an advanced dual functional cloning strategy, in which phagocytosis-based functional cloning is combined with receptor-based affinity cloning to directly identify receptor-specific eat-me signal. Gal-3 interaction with MerTK was independently verified by co-immunoprecipitation. Functional analyses showed that Gal-3 stimulated the phagocytosis of apoptotic cells and cellular debris by macrophages and retinal pigment epithelial cells with MerTK activation and autophosphorylation. The Gal-3-mediated phagocytosis was blocked by excessive soluble MerTK extracellular domain and lactose. These results suggest that Gal-3 is a legitimate MerTK-specific eat-me signal. The strategy of dual functional cloning with applicability to other phagocytic receptors will facilitate unbiased identification of their unknown ligands and improve our capacity for therapeutic modulation of phagocytic activity and innate immune response.
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Affiliation(s)
- Nora B Caberoy
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, Florida 33136, USA
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Larman HB, Zhao Z, Laserson U, Li MZ, Ciccia A, Gakidis MAM, Church GM, Kesari S, Leproust EM, Solimini NL, Elledge SJ. Autoantigen discovery with a synthetic human peptidome. Nat Biotechnol 2011; 29:535-41. [PMID: 21602805 PMCID: PMC4169279 DOI: 10.1038/nbt.1856] [Citation(s) in RCA: 215] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/28/2011] [Indexed: 02/07/2023]
Abstract
Immune responses targeting self-proteins (autoantigens) can lead to a variety of autoimmune diseases. Identification of these antigens is important for both diagnostic and therapeutic reasons. However, current approaches to characterize autoantigens have, in most cases, met only with limited success. Here we present a synthetic representation of the complete human proteome, the T7 peptidome phage display library (T7-Pep), and demonstrate its application to autoantigen discovery. T7-Pep is composed of >413,000 36-residue, overlapping peptides that cover all open reading frames in the human genome, and can be analyzed using high-throughput DNA sequencing. We developed a phage immunoprecipitation sequencing (PhIP-Seq) methodology to identify known and previously unreported autoantibodies contained in the spinal fluid of three individuals with paraneoplastic neurological syndromes. We also show how T7-Pep can be used more generally to identify peptide-protein interactions, suggesting the broader utility of our approach for proteomic research.
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Affiliation(s)
- H Benjamin Larman
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
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Identification of calpain substrates by ORF phage display. Molecules 2011; 16:1739-48. [PMID: 21339709 PMCID: PMC3175615 DOI: 10.3390/molecules16021739] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 02/18/2011] [Indexed: 11/17/2022] Open
Abstract
Substrate identification is the key to defining molecular pathways or cellular processes regulated by proteases. Although phage display with random peptide libraries has been used to analyze substrate specificity of proteases, it is difficult to deduce endogenous substrates from mapped peptide motifs. Phage display with conventional cDNA libraries identifies high percentage of non-open reading frame (non-ORF) clones, which encode short unnatural peptides, owing to uncontrollable reading frames of cellular proteins. We recently developed ORF phage display to identify endogenous proteins with specific binding or functional activity with minimal reading frame problem. Here we used calpain 2 as a protease to demonstrate that ORF phage display is capable of identifying endogenous substrates and showed its advantage to re-verify and characterize the identified substrates without requiring pure substrate proteins. An ORF phage display cDNA library with C-terminal biotin was bound to immobilized streptavidin and released by cleavage with calpain 2. After three rounds of phage selection, eleven substrates were identified, including calpastatin of endogenous calpain inhibitor. These results suggest that ORF phage display is a valuable technology to identify endogenous substrates for proteases.
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