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Sarabia I, Koss KM. Search for microglia-specific peptides: advances in the discovery toolbox. Neural Regen Res 2025; 20:471-472. [PMID: 38819052 PMCID: PMC11317953 DOI: 10.4103/nrr.nrr-d-24-00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/08/2024] [Accepted: 03/21/2024] [Indexed: 06/01/2024] Open
Affiliation(s)
- Ivan Sarabia
- Department of Surgery, University of Arizona, Tucson, AZ, USA
| | - Kyle M. Koss
- Department of Surgery, University of Arizona, Tucson, AZ, USA
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2
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Cham LB, Adomati T, Li F, Ali M, Lang KS. CD47 as a Potential Target to Therapy for Infectious Diseases. Antibodies (Basel) 2020; 9:antib9030044. [PMID: 32882841 PMCID: PMC7551396 DOI: 10.3390/antib9030044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
The integrin associated protein (CD47) is a widely and moderately expressed glycoprotein in all healthy cells. Cancer cells are known to induce increased CD47 expression. Similar to cancer cells, all immune cells can upregulate their CD47 surface expression during infection. The CD47-SIRPa interaction induces an inhibitory effect on macrophages and dendritic cells (dendritic cells) while CD47-thrombospondin-signaling inhibits T cells. Therefore, the disruption of the CD47 interaction can mediate several biologic functions. Upon the blockade and knockout of CD47 reveals an immunosuppressive effect of CD47 during LCMV, influenza virus, HIV-1, mycobacterium tuberculosis, plasmodium and other bacterial pneumonia infections. In our recent study we shows that the blockade of CD47 using the anti-CD47 antibody increases the activation and effector function of macrophages, dendritic cells and T cells during viral infection. By enhancing both innate and adaptive immunity, CD47 blocking antibody promotes antiviral effect. Due to its broad mode of action, the immune-stimulatory effect derived from this antibody could be applicable in nonresolving and (re)emerging infections. The anti-CD47 antibody is currently under clinical trial for the treatment of cancer and could also have amenable therapeutic potential against infectious diseases. This review highlights the immunotherapeutic targeted role of CD47 in the infectious disease realm.
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Rong X, Tian H, Yang L, Li W. Function-first ligandomics for ocular vascular research and drug target discovery. Exp Eye Res 2019; 182:57-64. [PMID: 30904565 DOI: 10.1016/j.exer.2019.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 12/29/2022]
Abstract
Human eyes may develop different vascular diseases with neovascularization and/or leakage, including wet age-related macular degeneration (AMD), diabetic macular edema (DME), proliferative diabetic retinopathy (PDR), retinopathy of prematurity, corneal neovascularization and intraocular tumors. A breakthrough in therapy is the advent and approval of vascular endothelial growth factor (VEGF) inhibitors. However, anti-VEGF drugs not only have limited efficacy to treat AMD, DME and PDR but also are not approved for other ocular indications. The key to addressing these unmet clinical needs is to develop novel therapies against VEGF-independent angiogenic factors or signaling pathways for alternative or combination therapy. We recently developed the first paradigm of ligandomics for global mapping of cell-wide ligands as well as disease-selective ligands. Therapies targeting disease-selective angiogenic or vascular leakage factors likely have high efficacy, minimal side effects, wide therapeutic windows and relatively low drug attrition rates. A critical challenge is how to distinguish between genuine drug targets and spurious hits identified by high-throughput ligandomics. Here we exploited the unique advantages of the eye and extracellular ligands by combining ligandomics with "function-first" and/or "therapy-first" analyses to efficiently characterize functional activity, disease selectivity, pathogenic role and therapeutic potential of identified ligands. The innovative function- or therapy-first ligandomics will systematically and reliably delineate disease-selective angiogenic or vascular leakage factors and markedly facilitate ocular vascular research and ligand-guided targeted anti-angiogenic therapy.
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Affiliation(s)
- Xin Rong
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Ophthalmology, Peking University First Hospital, Beijing, China
| | | | - Liu Yang
- Department of Ophthalmology, Peking University First Hospital, Beijing, China
| | - Wei Li
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA.
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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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5
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Mesd extrinsically promotes phagocytosis by retinal pigment epithelial cells. Cell Biol Toxicol 2016; 32:347-58. [PMID: 27184668 DOI: 10.1007/s10565-016-9339-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/09/2016] [Indexed: 01/09/2023]
Abstract
Phagocytosis is a critical process to maintain tissue homeostasis. In the retina, photoreceptor cells renew their photoexcitability by shedding photoreceptor outer segments (POSs) in a diurnal rhythm. Shed POSs are phagocytosed by retinal pigment epithelial (RPE) cells to prevent debris accumulation, retinal degeneration, and blindness. Phagocytosis ligands are the key to understanding how RPE recognizes shed POSs. Here, we characterized mesoderm development candidate 2 (Mesd or Mesdc2), an endoplasmic reticulum (ER) chaperon for low-density lipoprotein receptor-related proteins (LRPs), to extrinsically promote RPE phagocytosis. The results showed that Mesd stimulated phagocytosis of fluorescence-labeled POS vesicles by D407 RPE cells. Ingested POSs were partially degraded within 3 h in some RPE cells to dispense undegradable fluorophore throughout the cytoplasm. Internalized POSs were colocalized with phagosome biomarker Rab7, suggesting that Mesd-mediated engulfment is involved in a phagocytosis pathway. Mesd also facilitated phagocytosis of POSs by primary RPE cells. Mesd bound to unknown phagocytic receptor(s) on RPE cells. Mesd was detected in the cytoplasm, but not nuclei, of different retinal layers and is predominantly expressed in the ER-free cellular compartment of POSs. Mesd was not secreted into medium from healthy cells but passively released from apoptotic cells with increased membrane permeability. Released Mesd selectively bound to the surface of POS vesicles and apoptotic cells, but not healthy cells. These results suggest that Mesd may be released from and bind to shed POSs to facilitate their phagocytic clearance.
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6
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Ding Y, Caberoy NB, Guo F, LeBlanc ME, Zhang C, Wang W, Wang F, Chen R, Li W. Reticulocalbin-1 facilitates microglial phagocytosis. PLoS One 2015; 10:e0126993. [PMID: 25992960 PMCID: PMC4436338 DOI: 10.1371/journal.pone.0126993] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 04/09/2015] [Indexed: 12/26/2022] Open
Abstract
Phagocytosis is critical to the clearance of apoptotic cells, cellular debris and deleterious metabolic products for tissue homeostasis. Phagocytosis ligands directly recognizing deleterious cargos are the key to defining the functional roles of phagocytes, but are traditionally identified on a case-by-case basis with technical challenges. As a result, extrinsic regulation of phagocytosis is poorly defined. Here we demonstrate that microglial phagocytosis ligands can be systematically identified by a new approach of functional screening. One of the identified ligands is reticulocalbin-1 (Rcn1), which was originally reported as a Ca2+-binding protein with a strict expression in the endoplasmic reticulum. Our results showed that Rcn1 can be secreted from healthy cells and that secreted Rcn1 selectively bound to the surface of apoptotic neurons, but not healthy neurons. Independent characterization revealed that Rcn1 stimulated microglial phagocytosis of apoptotic but not healthy neurons. Ingested apoptotic cells were targeted to phagosomes and co-localized with phagosome marker Rab7. These data suggest that Rcn1 is a genuine phagocytosis ligand. The new approach described in this study will enable systematic identification of microglial phagocytosis ligands with broad applicability to many other phagocytes.
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Affiliation(s)
- Ying Ding
- Bascom Palmer Eye Institute, Dept. of Ophthalmology, University of Miami School of Medicine, Miami, FL, 33136, United States of America
| | - Nora B. Caberoy
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, United States of America
| | - Feiye Guo
- Bascom Palmer Eye Institute, Dept. of Ophthalmology, University of Miami School of Medicine, Miami, FL, 33136, United States of America
| | - Michelle E. LeBlanc
- Bascom Palmer Eye Institute, Dept. of Ophthalmology, University of Miami School of Medicine, Miami, FL, 33136, United States of America
| | - Chenming Zhang
- Bascom Palmer Eye Institute, Dept. of Ophthalmology, University of Miami School of Medicine, Miami, FL, 33136, United States of America
- Jinan 2 People’s Hospital, Jinan, 250001, China
| | - Weiwen Wang
- Bascom Palmer Eye Institute, Dept. of Ophthalmology, University of Miami School of Medicine, Miami, FL, 33136, United States of America
| | - Feng Wang
- Dept. of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, United States of America
| | - Rui Chen
- Dept. of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, United States of America
| | - Wei Li
- Bascom Palmer Eye Institute, Dept. of Ophthalmology, University of Miami School of Medicine, Miami, FL, 33136, United States of America
- Neuroscience Program, University of Miami School of Medicine, Miami, FL, 33136, United States of America
- * E-mail:
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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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8
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Li HM, Guo K, Yu Z, Feng R, Xu P. Diagnostic value of protein chips constructed by lung-cancer-associated markers selected by the T7 phage display library. Thorac Cancer 2015; 6:469-74. [PMID: 26273403 PMCID: PMC4511326 DOI: 10.1111/1759-7714.12215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/05/2014] [Indexed: 12/17/2022] Open
Abstract
Background Traditional diagnostic technology with tumor biomarkers is inefficient, expensive and requires a large number of serum samples. The purpose of this study was to construct human lung cancer protein chips with new lung cancer biomarkers screened by the T7-phage display library, and improve the early diagnosis rate of lung cancer. Methods A T7-phage cDNA display library was constructed of fresh samples from 30 lung cancer patients. With biopanning and high-throughput screening, we gained the immunogenic phage clones from the cDNA library. The insert of selected phage was blasted at GeneBank for alignment to find the exact or the most similar known genes. Protein chips were then constructed and used to assay their expression level in lung cancer serum from 217 cases of lung cancer groups:80 cases of benign lung disease and 220 healthy controls. Results After four rounds of Biopanning and two rounds of enzyme-linked immunosorbent assay, 12 phage monoclonal samples were selected from 2880 phage monoclonal samples. After blasting at GeneBank, six similar genes were used to construct diagnostic protein chips. The protein chips were then used to assay expression level in lung cancer serum. The expression level of six genes in lung cancer groups was significantly higher than those in the other two groups (P < 0.05). Conclusions In this study, we successfully constructed diagnostic protein chips with biomarkers selected from the lung cancer T7-phage cDNA library, which can be used for the early screening of lung cancer patients.
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Affiliation(s)
- Hong-Mei Li
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
| | - Kang Guo
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
| | - Zhuang Yu
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
| | - Rui Feng
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
| | - Ping Xu
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
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9
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Caberoy NB, Alvarado G, Li W. Tubby regulates microglial phagocytosis through MerTK. J Neuroimmunol 2012; 252:40-8. [PMID: 22884297 DOI: 10.1016/j.jneuroim.2012.07.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/02/2012] [Accepted: 07/19/2012] [Indexed: 02/03/2023]
Abstract
Immunologically-silent microglial phagocytosis of apoptotic cells and cellular debris is critical for CNS homeostasis and innate immune balance. The beneficial and detrimental effects of microglial phagocytosis on neurons remain controversial. Phagocytosis ligands are the key to selecting extracellular cargos, initiating the engulfment process, defining phagocyte functional roles and regulating phagocyte activities with therapeutic potentials. Here we characterized tubby as a new ligand to regulate microglial phagocytosis through MerTK receptor, which is well known for its immunosuppressive signaling. Tubby at 0.1nM significantly induced microglial phagocytosis of apoptotic cells with a maximal activity at 10nM. Tubby activated MerTK with receptor autophosphorylation in a similar dose range. Excessive soluble MerTK extracellular domain blocked tubby-mediated microglial phagocytosis of plasma membrane vesicles as cellular debris. Immunocytochemistry revealed that the ingested cargos were co-localized with MerTK-dependent non-muscle myosin II, whose rearrangement is necessary for cargo engulfment. Phagosome biomarker Rab7 was colocalized with cargos, suggesting that internalized cargos were targeted to phagocytic pathway. Tubby stimulated phagocytosis by neonatal and aged microglia with similar activities, but not by MerTK(-/-) microglia. These results suggest that tubby is a ligand to facilitate microglial phagocytosis through MerTK for the maintenance of CNS homeostasis.
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Affiliation(s)
- Nora B Caberoy
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL 33136, USA
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Abstract
INTRODUCTION The interpretation of high-throughput profiling data depends on the pathway analysis database. Currently, pathway analysis often has to rely on a set of interactions and pathways measured in every possible human tissue, due to insufficient knowledge about interactions and pathways in the context of the profiling experiment. However, a recent global scale analysis of human tissue proteomes and interactomes reveals significant differences among tissues, suggesting that interaction and pathway data that are used out of biological context are the major source of inaccuracies and noise in the analysis of profiling data. AREAS COVERED In this review, the major classes of biological context used for experimental detection of molecular interactions and pathways in molecular biology are described. Furthermore, the author reviews methods for predicting biological interactions in order to evaluate the applicability of various contextual interaction data in pathway analysis. Using the results from recent publications that study large-scale tissue composition, the article provides an estimation of the gain in pathway analysis accuracy if only the interactions predicted for the context of a molecular profiling experiment are used, relative to the analysis performed with a context-independent knowledge base. EXPERT OPINION It is of the author's opinion that the major source of inaccuracy in pathway analysis is the lack of knowledge about tissue-specific transcriptional regulation. It is therefore suggested that the accuracy of the analysis can be substantially improved if only context-specific interactions and pathways are used for interpretation.
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Affiliation(s)
- Anton Yuryev
- Elsevier, Ariadne Genomics, Inc., Rockville, MD 20878, USA.
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11
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Li W. Eat-me signals: keys to molecular phagocyte biology and "appetite" control. J Cell Physiol 2012; 227:1291-7. [PMID: 21520079 DOI: 10.1002/jcp.22815] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hundreds of billions of cells undergo apoptosis in our body everyday and are removed by immunologically silent phagocytosis to maintain tissue homeostasis. Impairments in phagocytosis result in autoimmune and/or degenerative diseases. Eat-me signals are the key to the recognition of extracellular cargos and the initiation of the phagocytosis process by activating phagocytic receptors and signaling cascades, and are convenient targets for therapeutic modulation. Despite their importance, eat-me signals and other phagocytosis players are mostly identified on case-by-case basis with daunting challenges. This Commentary focuses on our latest knowledge of the extracellular players, highlights our approaches to systematically map unknown pathways by functional genetic and proteomic technologies, and discusses future direction to unravel the mystery of molecular phagocyte biology.
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Affiliation(s)
- Wei Li
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, Florida 33136, USA.
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12
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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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Unraveling the molecular mystery of retinal pigment epithelium phagocytosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 723:693-9. [PMID: 22183395 PMCID: PMC4096043 DOI: 10.1007/978-1-4614-0631-0_88] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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14
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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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Caberoy NB, Zhou Y, Li W. Tubby and tubby-like protein 1 are new MerTK ligands for phagocytosis. EMBO J 2010; 29:3898-910. [PMID: 20978472 DOI: 10.1038/emboj.2010.265] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 09/27/2010] [Indexed: 12/29/2022] Open
Abstract
Tubby and tubby-like protein 1 (Tulp1) are newly identified phagocytosis ligands to facilitate retinal pigment epithelium (RPE) and macrophage phagocytosis. Both proteins without classical signal peptide have been demonstrated with unconventional secretion. Here, we characterized them as novel MerTK ligands to facilitate phagocytosis. Tulp1 interacts with Tyro3, Axl and MerTK of the TAM receptor tyrosine kinase subfamily, whereas tubby binds only to MerTK. Excessive soluble MerTK extracellular domain blocked tubby- or Tulp1-mediated phagocytosis. Both ligands induced MerTK activation with receptor phosphorylation and signalling cascade, including non-muscle myosin II redistribution and co-localization with phagosomes. Tubby and Tulp1 are bridging molecules with their N-terminal region as MerTK-binding domain and C-terminal region as phagocytosis prey-binding domain (PPBD). Five minimal phagocytic determinants (MPDs) of K/R(X)(1-2)KKK in Tulp1 N-terminus were defined as essential motifs for MerTK binding, receptor phosphorylation and phagocytosis. PPBD was mapped to the highly conserved 54 amino acids at the C-terminal end of tubby and Tulp1. These data suggest that tubby and Tulp1 are novel bridging molecules to facilitate phagocytosis through MerTK.
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Affiliation(s)
- Nora B Caberoy
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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16
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Caberoy NB, Zhou Y, Jiang X, Alvarado G, Li W. Efficient identification of tubby-binding proteins by an improved system of T7 phage display. J Mol Recognit 2010; 23:74-83. [PMID: 19718693 DOI: 10.1002/jmr.983] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mutation in the tubby gene causes adult-onset obesity, progressive retinal, and cochlear degeneration with unknown mechanism. In contrast, mutations in tubby-like protein 1 (Tulp1), whose C-terminus is highly homologous to tubby, only lead to retinal degeneration. We speculate that their diverse N-terminus may define their distinct disease profile. To elucidate the binding partners of tubby, we used tubby N-terminus (tubby-N) as bait to identify unknown binding proteins with open-reading-frame (ORF) phage display. T7 phage display was engineered with three improvements: high-quality ORF phage display cDNA library, specific phage elution by protease cleavage, and dual phage display for sensitive high throughput screening. The new system is capable of identifying unknown bait-binding proteins in as fast as approximately 4-7 days. While phage display with conventional cDNA libraries identifies high percentage of out-of-frame unnatural short peptides, all 28 tubby-N-binding clones identified by ORF phage display were ORFs. They encode 16 proteins, including 8 nuclear proteins. Fourteen proteins were analyzed by yeast two-hybrid assay and protein pull-down assay with ten of them independently verified. Comparative binding analyses revealed several proteins binding to both tubby and Tulp1 as well as one tubby-specific binding protein. These data suggest that tubby-N is capable of interacting with multiple nuclear and cytoplasmic protein binding partners. These results demonstrated that the newly-engineered ORF phage display is a powerful technology to identify unknown protein-protein interactions.
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Affiliation(s)
- Nora B Caberoy
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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Caberoy NB, Maiguel D, Kim Y, Li W. Identification of tubby and tubby-like protein 1 as eat-me signals by phage display. Exp Cell Res 2009; 316:245-57. [PMID: 19837063 DOI: 10.1016/j.yexcr.2009.10.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 09/10/2009] [Accepted: 10/07/2009] [Indexed: 01/24/2023]
Abstract
Phagocytosis is an important process for the removal of apoptotic cells or cellular debris. Eat-me signals control the initiation of phagocytosis and hold the key for in-depth understanding of its molecular mechanisms. However, because of difficulties to identify unknown eat-me signals, only a limited number of them have been identified and characterized. Using a newly developed functional cloning strategy of open reading frame (ORF) phage display, we identified nine putative eat-me signals, including tubby-like protein 1 (Tulp1). This further led to the elucidation of tubby as the second eat-me signal in the same protein family. Both proteins stimulated phagocytosis of retinal pigment epithelium (RPE) cells and macrophages. Tubby-conjugated fluorescent microbeads facilitated RPE phagocytosis. Tubby and Tulp1, but not other family members, enhanced the uptake of membrane vesicles by RPE cells in synergy. Retinal membrane vesicles of Tubby mice and Tulp1(-/-) mice showed reduced activities for RPE phagocytosis, which were compensated by purified tubby and Tulp1, respectively. These data reveal a novel activity of tubby and Tulp1, and demonstrate that unbiased identification of eat-me signals by the broadly applicable strategy of ORF phage display can provide detailed insights into phagocyte biology.
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Affiliation(s)
- Nora B Caberoy
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Miami, FL 33136, USA
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New perspective for phage display as an efficient and versatile technology of functional proteomics. Appl Microbiol Biotechnol 2009; 85:909-19. [PMID: 19885657 DOI: 10.1007/s00253-009-2277-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 09/23/2009] [Accepted: 09/23/2009] [Indexed: 10/20/2022]
Abstract
Phage display with antibody libraries has been widely used with versatile applications. However, phage display with cDNA libraries is rare and inefficient. Because of uncontrollable reading frames and stop codons in cDNA repertoires, high percentage of phage clones identified from conventional cDNA libraries are non-open reading frames (non-ORFs) encoding unnatural short peptides with minimal implications in protein networks. Consequently, phage display has not been used as a technology of functional proteomics to elucidate protein-protein interactions like yeast two-hybrid system and mass spectrometry-based technologies. Several strategies, including C-terminal display and ORF cDNA libraries, have been explored to circumvent the technical problem. The accumulative endeavors eventually led to the efficient elucidation of a large number of tubby- and phosphatidylserine-binding proteins in recent studies by ORF phage display with minimal reading frame issue. ORF phage display inherits all the versatile applications of antibody phage display, but enables efficient identification of real endogenous proteins with efficiency, sensitivity, and accuracy comparable to other technologies of functional proteomics. Its ELISA-like procedure can be conveniently adapted by individual laboratories or fully automated for high-throughput screening. Thus, ORF phage display is an efficient, sensitive, versatile, and convenient technology of functional proteomics for elucidation of global and pathway-specific protein-protein interactions, disease mechanisms, or therapeutic targets.
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Caberoy NB, Li W. Unconventional secretion of tubby and tubby-like protein 1. FEBS Lett 2009; 583:3057-62. [PMID: 19695251 DOI: 10.1016/j.febslet.2009.08.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Revised: 08/10/2009] [Accepted: 08/11/2009] [Indexed: 12/24/2022]
Abstract
Tubby-like proteins (Tulps) with no signal peptide have been characterized as cytoplasmic proteins with various intracellular functions, including binding to phosphatidylinositol-4,5-bisphosphate [PI(4,5)P(2)]. PI(4,5)P(2) has been implicated in unconventional secretion of fibroblast growth factor-2 without a signal peptide. Here, we show that all Tulps are expressed intracellularly and extracellularly. Tubby secretion is partially dependent on its PI(4,5)P(2)-binding activity with an essential secretory signal in the N-terminus. Pathogenic mutation in Tubby mice has no impact on tubby extracellular trafficking. Moreover, unconventional secretion of tubby and Tulp1 is independent of endoplasmic reticulum-Golgi pathway. These data implicate that Tulps may function extracellularly as well.
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Affiliation(s)
- Nora B Caberoy
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, FL 33136, USA
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Efficient identification of phosphatidylserine-binding proteins by ORF phage display. Biochem Biophys Res Commun 2009; 386:197-201. [PMID: 19520055 DOI: 10.1016/j.bbrc.2009.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 06/05/2009] [Indexed: 12/28/2022]
Abstract
To efficiently elucidate the biological roles of phosphatidylserine (PS), we developed open-reading-frame (ORF) phage display to identify PS-binding proteins. The procedure of phage panning was optimized with a phage clone expressing MFG-E8, a well-known PS-binding protein. Three rounds of phage panning with ORF phage display cDNA library resulted in approximately 300-fold enrichment in PS-binding activity. A total of 17 PS-binding phage clones were identified. Unlike phage display with conventional cDNA libraries, all 17 PS-binding clones were ORFs encoding 13 real proteins. Sequence analysis revealed that all identified PS-specific phage clones had dimeric basic amino acid residues. GST fusion proteins were expressed for 3 PS-binding proteins and verified for their binding activity to PS liposomes, but not phosphatidylcholine liposomes. These results elucidated previously unknown PS-binding proteins and demonstrated that ORF phage display is a versatile technology capable of efficiently identifying binding proteins for non-protein molecules like PS.
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