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Wat LW, Svensson KJ. Novel secreted regulators of glucose and lipid metabolism in the development of metabolic diseases. Diabetologia 2024:10.1007/s00125-024-06253-x. [PMID: 39180580 DOI: 10.1007/s00125-024-06253-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/01/2024] [Indexed: 08/26/2024]
Abstract
The tight regulation of glucose and lipid metabolism is crucial for maintaining metabolic health. Dysregulation of these processes can lead to the development of metabolic diseases. Secreted factors, or hormones, play an essential role in the regulation of glucose and lipid metabolism, thus also playing an important role in the development of metabolic diseases such as type 2 diabetes and obesity. Given the important roles of secreted factors, there has been significant interest in identifying new secreted factors and new functions for existing secreted factors that control glucose and lipid metabolism. In this review, we evaluate novel secreted factors or novel functions of existing factors that regulate glucose and lipid metabolism discovered in the last decade, including secreted isoform of endoplasmic reticulum membrane complex subunit 10, vimentin, cartilage intermediate layer protein 2, isthmin-1, lipocalin-2, neuregulin-1 and neuregulin-4. We discuss their discovery, tissues of origin, mechanisms of action and sex differences, emphasising their potential to regulate metabolic processes central to diabetes. Additionally, we discuss the translational barriers, particularly the absence of identified receptors, that hamper their functional characterisation and further therapeutic development. Ultimately, the identification of new secreted factors may give insights into previously unidentified pathways of disease progression and mechanisms of glucose and lipid homeostasis.
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Affiliation(s)
- Lianna W Wat
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Katrin J Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
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2
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Shilts J, Wright GJ. Mapping the Human Cell Surface Interactome: A Key to Decode Cell-to-Cell Communication. Annu Rev Biomed Data Sci 2024; 7:155-177. [PMID: 38723658 DOI: 10.1146/annurev-biodatasci-102523-103821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2024]
Abstract
Proteins on the surfaces of cells serve as physical connection points to bridge one cell with another, enabling direct communication between cells and cohesive structure. As biomedical research makes the leap from characterizing individual cells toward understanding the multicellular organization of the human body, the binding interactions between molecules on the surfaces of cells are foundational both for computational models and for clinical efforts to exploit these influential receptor pathways. To achieve this grander vision, we must assemble the full interactome of ways surface proteins can link together. This review investigates how close we are to knowing the human cell surface protein interactome. We summarize the current state of databases and systematic technologies to assemble surface protein interactomes, while highlighting substantial gaps that remain. We aim for this to serve as a road map for eventually building a more robust picture of the human cell surface protein interactome.
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Affiliation(s)
- Jarrod Shilts
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom;
- School of the Biological Sciences, University of Cambridge, Cambridge, United Kingdom;
| | - Gavin J Wright
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom;
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3
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Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science 2024; 385:eadl5763. [PMID: 39024454 DOI: 10.1126/science.adl5763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
Proximity labeling proteomics (PLP) strategies are powerful approaches to yield snapshots of protein neighborhoods. Here, we describe a multiscale PLP method with adjustable resolution that uses a commercially available photocatalyst, Eosin Y, which upon visible light illumination activates different photo-probes with a range of labeling radii. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor and orthogonally validated more than 20 neighbors using immunoassays and AlphaFold-Multimer prediction. We further profiled the protein neighborhoods of cell-cell synapses induced by bispecific T cell engagers and chimeric antigen receptor T cells. This integrated multiscale PLP platform maps local and distal protein networks on and between cell surfaces, which will aid in the systematic construction of the cell surface interactome, revealing horizontal signaling partners and reveal new immunotherapeutic opportunities.
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Affiliation(s)
- Zhi Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kaitlin Schaefer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zi Yao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrea Fossati
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ajikarunia Palar
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
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4
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Jobe A, Vijayan R. Orphan G protein-coupled receptors: the ongoing search for a home. Front Pharmacol 2024; 15:1349097. [PMID: 38495099 PMCID: PMC10941346 DOI: 10.3389/fphar.2024.1349097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/19/2024] Open
Abstract
G protein-coupled receptors (GPCRs) make up the largest receptor superfamily, accounting for 4% of protein-coding genes. Despite the prevalence of such transmembrane receptors, a significant number remain orphans, lacking identified endogenous ligands. Since their conception, the reverse pharmacology approach has been used to characterize such receptors. However, the multifaceted and nuanced nature of GPCR signaling poses a great challenge to their pharmacological elucidation. Considering their therapeutic relevance, the search for native orphan GPCR ligands continues. Despite limited structural input in terms of 3D crystallized structures, with advances in machine-learning approaches, there has been great progress with respect to accurate ligand prediction. Though such an approach proves valuable given that ligand scarcity is the greatest hurdle to orphan GPCR deorphanization, the future pairings of the remaining orphan GPCRs may not necessarily take a one-size-fits-all approach but should be more comprehensive in accounting for numerous nuanced possibilities to cover the full spectrum of GPCR signaling.
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Affiliation(s)
- Amie Jobe
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- The Big Data Analytics Center, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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5
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Yang L, Sheets TP, Feng Y, Yu G, Bajgain P, Hsu KS, So D, Seaman S, Lee J, Lin L, Evans CN, Guest MR, Chari R, St. Croix B. Uncovering receptor-ligand interactions using a high-avidity CRISPR activation screening platform. SCIENCE ADVANCES 2024; 10:eadj2445. [PMID: 38354234 PMCID: PMC10866537 DOI: 10.1126/sciadv.adj2445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The majority of clinically approved drugs target proteins that are secreted or cell surface bound. However, further advances in this area have been hindered by the challenging nature of receptor deorphanization, as there are still many secreted and cell-bound proteins with unknown binding partners. Here, we developed an advanced screening platform that combines CRISPR-CAS9 guide-mediated gene activation (CRISPRa) and high-avidity bead-based selection. The CRISPRa platform incorporates serial enrichment and flow cytometry-based monitoring, resulting in substantially improved screening sensitivity for well-known yet weak interactions of the checkpoint inhibitor family. Our approach has successfully revealed that siglec-4 exerts regulatory control over T cell activation through a low affinity trans-interaction with the costimulatory receptor 4-1BB. Our highly efficient screening platform holds great promise for identifying extracellular interactions of uncharacterized receptor-ligand partners, which is essential to develop next-generation therapeutics, including additional immune checkpoint inhibitors.
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Affiliation(s)
- Liping Yang
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Timothy P. Sheets
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Yang Feng
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Guojun Yu
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Pradip Bajgain
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Kuo-Sheng Hsu
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Daeho So
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Steven Seaman
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Jaewon Lee
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
| | - Ling Lin
- Proteomic Instability of Cancer Section, MCGP, NCI, NIH, Frederick, MD 21702, USA
| | - Christine N. Evans
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Mary R. Guest
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Brad St. Croix
- Tumor Angiogenesis Unit, Mouse Cancer Genetics Program (MCGP), National Cancer Institute (NCI), NIH, Frederick, MD 21702, USA
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Sollazzo G, Nikolouli K, Gouvi G, Aumann RA, Schetelig MF, Bourtzis K. Deep orange gene editing triggers temperature-sensitive lethal phenotypes in Ceratitis capitata. BMC Biotechnol 2024; 24:7. [PMID: 38302991 PMCID: PMC10835909 DOI: 10.1186/s12896-024-00832-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND The Mediterranean fruit fly, Ceratitis capitata, is a significant agricultural pest managed through area-wide integrated pest management (AW-IPM) including a sterile insect technique (SIT) component. Male-only releases increase the efficiency and cost-effectiveness of SIT programs, which can be achieved through the development of genetic sexing strains (GSS). The most successful GSS developed to date is the C. capitata VIENNA 8 GSS, constructed using classical genetic approaches and an irradiation-induced translocation with two selectable markers: the white pupae (wp) and temperature-sensitive lethal (tsl) genes. However, currently used methods for selecting suitable markers and inducing translocations are stochastic and non-specific, resulting in a laborious and time-consuming process. Recent efforts have focused on identifying the gene(s) and the causal mutation(s) for suitable phenotypes, such as wp and tsl, which could be used as selectable markers for developing a generic approach for constructing GSS. The wp gene was recently identified, and efforts have been initiated to identify the tsl gene. This study investigates Ceratitis capitata deep orange (Ccdor) as a tsl candidate gene and its potential to induce tsl phenotypes. RESULTS An integrated approach based on cytogenetics, genomics, bioinformatics, and gene editing was used to characterize the Ccdor. Its location was confirmed on the right arm of chromosome 5 in the putative tsl genomic region. Knock-out of Ccdor using CRISPR/Cas9-NHEJ and targeting the fourth exon resulted in lethality at mid- and late-pupal stage, while the successful application of CRISPR HDR introducing a point mutation on the sixth exon resulted in the establishment of the desired strain and two additional strains (dor 12del and dor 51dup), all of them expressing tsl phenotypes and presenting no (or minimal) fitness cost when reared at 25 °C. One of the strains exhibited complete lethality when embryos were exposed at 36 °C. CONCLUSIONS Gene editing of the deep orange gene in Ceratitis capitata resulted in the establishment of temperature-sensitive lethal mutant strains. The induced mutations did not significantly affect the rearing efficiency of the strains. As deep orange is a highly conserved gene, these data suggest that it can be considered a target for the development of tsl mutations which could potentially be used to develop novel genetic sexing strains in insect pests and disease vectors.
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Affiliation(s)
- Germano Sollazzo
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Friedensstrasse 1, Seibersdorf, 2444, Austria
- Institute for Insect Biotechnology, Department of Insect Biotechnology in Plant Protection, Justus-Liebig-University Gießen, Winchesterstr. 2, Gießen, 35394, Germany
- Present address: Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, Imperial College Road, London, SW7 2AZ, UK
| | - Katerina Nikolouli
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Friedensstrasse 1, Seibersdorf, 2444, Austria
| | - Georgia Gouvi
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Friedensstrasse 1, Seibersdorf, 2444, Austria
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, 2 G. Seferi St., Agrinio, 30100, Greece
- Present address: Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, Imperial College Road, London, SW7 2AZ, UK
| | - Roswitha A Aumann
- Institute for Insect Biotechnology, Department of Insect Biotechnology in Plant Protection, Justus-Liebig-University Gießen, Winchesterstr. 2, Gießen, 35394, Germany
| | - Marc F Schetelig
- Institute for Insect Biotechnology, Department of Insect Biotechnology in Plant Protection, Justus-Liebig-University Gießen, Winchesterstr. 2, Gießen, 35394, Germany.
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Friedensstrasse 1, Seibersdorf, 2444, Austria.
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Danneskiold-Samsøe NB, Kavi D, Jude KM, Nissen SB, Wat LW, Coassolo L, Zhao M, Santana-Oikawa GA, Broido BB, Garcia KC, Svensson KJ. AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.531341. [PMID: 36993313 PMCID: PMC10055078 DOI: 10.1101/2023.03.16.531341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Secreted proteins play crucial roles in paracrine and endocrine signaling; however, identifying novel ligand-receptor interactions remains challenging. Here, we benchmarked AlphaFold as a screening approach to identify extracellular ligand-binding pairs using a structural library of single-pass transmembrane receptors. Key to the approach is the optimization of AlphaFold input and output for screening ligands against receptors to predict the most probable ligand-receptor interactions. Importantly, the predictions were performed on ligand-receptor pairs not used for AlphaFold training. We demonstrate high discriminatory power and a success rate of close to 90 % for known ligand-receptor pairs and 50 % for a diverse set of experimentally validated interactions. These results demonstrate proof-of-concept of a rapid and accurate screening platform to predict high-confidence cell-surface receptors for a diverse set of ligands by structural binding prediction, with potentially wide applicability for the understanding of cell-cell communication.
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Affiliation(s)
- Niels Banhos Danneskiold-Samsøe
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, University of Copenhagen, Denmark
| | - Deniz Kavi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Silas Boye Nissen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Lianna W. Wat
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Laetitia Coassolo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Meng Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Department of Structural Biology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Katrin J. Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA, USA
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8
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Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564055. [PMID: 37961561 PMCID: PMC10634877 DOI: 10.1101/2023.10.28.564055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The cell membrane proteome is the primary biohub for cell communication, yet we are only beginning to understand the dynamic protein neighborhoods that form on the cell surface and between cells. Proximity labeling proteomics (PLP) strategies using chemically reactive probes are powerful approaches to yield snapshots of protein neighborhoods but are currently limited to one single resolution based on the probe labeling radius. Here, we describe a multi-scale PLP method with tunable resolution using a commercially available histological dye, Eosin Y, which upon visible light illumination, activates three different photo-probes with labeling radii ranging from ∼100 to 3000 Å. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor (EGFR) and orthogonally validated >20 neighbors using immuno-assays and AlphaFold-Multimer prediction that generated plausible binary interaction models. We further profiled the protein neighborhoods of cell-cell synapses induced by bi-specific T-cell engagers (BiTEs) and chimeric antigen receptor (CAR)T cells at longer length scales. This integrated multi-scale PLP platform maps local and distal protein networks on cell surfaces and between cells. We believe this information will aid in the systematic construction of the cell surface interactome and reveal new opportunities for immunotherapeutics.
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9
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Bendixen L, Jensen TI, Bak RO. CRISPR-Cas-mediated transcriptional modulation: The therapeutic promises of CRISPRa and CRISPRi. Mol Ther 2023; 31:1920-1937. [PMID: 36964659 PMCID: PMC10362391 DOI: 10.1016/j.ymthe.2023.03.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
The CRISPR-Cas system is commonly known for its ability to cleave DNA in a programmable manner, which has democratized gene editing and facilitated recent breakthroughs in gene therapy. However, newer iterations of the technology using nuclease-disabled Cas enzymes have spurred a variety of different types of genetic engineering platforms such as transcriptional modulation using the CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) systems. This review introduces the creation of these programmable transcriptional modulators, various methods of delivery utilized for these systems, and recent technological developments. CRISPRa and CRISPRi have also been implemented in genetic screens for interrogating gene function and discovering genes involved in various biological pathways. We describe recent compelling examples of how these tools have become powerful means to unravel genetic networks and uncovering important information about devastating diseases. Finally, we provide an overview of preclinical studies in which transcriptional modulation has been used therapeutically, and we discuss potential future directions of these novel modalities.
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Affiliation(s)
- Louise Bendixen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Trine I Jensen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark.
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Siepe DH, Picton LK, Garcia KC. Receptor Elimination by E3 Ubiquitin Ligase Recruitment (REULR): A Targeted Protein Degradation Toolbox. ACS Synth Biol 2023; 12:1081-1093. [PMID: 37011906 PMCID: PMC10127277 DOI: 10.1021/acssynbio.2c00587] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Indexed: 04/05/2023]
Abstract
In recent years, targeted protein degradation (TPD) of plasma membrane proteins by hijacking the ubiquitin proteasome system (UPS) or the lysosomal pathway has emerged as a novel therapeutic avenue in drug development to address and inhibit canonically difficult targets. While TPD strategies have been successful in targeting cell surface receptors, these approaches are limited by the availability of suitable binders to generate heterobifunctional molecules. Here, we present the development of a nanobody (VHH)-based degradation toolbox termed REULR (Receptor Elimination by E3 Ubiquitin Ligase Recruitment). We generated human and mouse cross-reactive nanobodies against five transmembrane PA-TM-RING-type E3 ubiquitin ligases (RNF128, RNF130, RNF167, RNF43, and ZNRF3), covering a broad range and selectivity of tissue expression, with which we characterized the expression in human and mouse cell lines and immune cells (PBMCs). We demonstrate that heterobifunctional REULR molecules can enforce transmembrane E3 ligase interactions with a variety of disease-relevant target receptors (EGFR, EPOR, and PD-1) by induced proximity, resulting in effective membrane clearance of the target receptor at varying levels. In addition, we designed E3 ligase self-degrading molecules, "fratricide" REULRs (RNF128, RNF130, RENF167, RNF43, and ZNRF3), that allow downregulation of one or several E3 ligases from the cell surface and consequently modulate receptor signaling strength. REULR molecules represent a VHH-based modular and versatile "mix and match" targeting strategy for the facile modulation of cell surface proteins by induced proximity to transmembrane PA-TM-RING E3 ligases.
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Affiliation(s)
- Dirk H. Siepe
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
| | - Lora K. Picton
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
| | - K. Christopher Garcia
- Department
of Molecular and Cellular Physiology, Stanford
University School of Medicine, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Howard
Hughes Medical Institute, Stanford University
School of Medicine, Stanford, California 94305, United States
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