1
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Wang D, Wang Y. Identification of protein partners for small molecules reshapes the understanding of nonalcoholic steatohepatitis and drug discovery. Life Sci 2024; 356:123031. [PMID: 39226989 DOI: 10.1016/j.lfs.2024.123031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/16/2024] [Accepted: 08/30/2024] [Indexed: 09/05/2024]
Abstract
AIMS Nonalcoholic steatohepatitis (NASH) is the severe subtype of nonalcoholic fatty diseases (NAFLD) with few options for treatment. Patients with NASH exhibit partial responses to the current therapeutics and adverse effects. Identification of the binding proteins for the drugs is essential to understanding the mechanism and adverse effects of the drugs and fuels the discovery of potent and safe drugs. This paper aims to critically discuss recent advances in covalent and noncovalent approaches for identifying binding proteins that mediate NASH progression, along with an in-depth analysis of the mechanisms by which these targets regulate NASH. MATERIALS AND METHODS A literature search was conducted to identify the relevant studies in the database of PubMed and the American Chemical Society. The search covered articles published from January 1990 to July 2024, using the search terms with keywords such as NASH, benzophenone, diazirine, photo-affinity labeling, thermal protein profiling, CETSA, target identification. KEY FINDINGS The covalent approaches utilize drugs modified with diazirine and benzophenone to covalently crosslink with the target proteins, which facilitates the purification and identification of target proteins. In addition, they map the binding sites in the target proteins. By contrast, noncovalent approaches identify the binding targets of unmodified drugs in the intact cell proteome. The advantages and limitations of both approaches have been compared, along with a comprehensive analysis of recent innovations that further enhance the efficiency and specificity. SIGNIFICANCE The analyses of the applicability of these approaches provide novel tools to delineate NASH pathogenesis and promote drug discovery.
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Affiliation(s)
- Danyi Wang
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China
| | - Yibing Wang
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
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2
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Wogram E, Sümpelmann F, Dong W, Rawat E, Fernández Maestre I, Fu D, Braswell B, Khalil A, Buescher JM, Mittler G, Borner GHH, Vlachos A, Tholen S, Schilling O, Bell GW, Rambold AS, Akhtar A, Schnell O, Beck J, Abu-Remaileh M, Prinz M, Jaenisch R. Rapid phagosome isolation enables unbiased multiomic analysis of human microglial phagosomes. Immunity 2024; 57:2216-2231.e11. [PMID: 39151426 DOI: 10.1016/j.immuni.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/25/2024] [Accepted: 07/19/2024] [Indexed: 08/19/2024]
Abstract
Microglia are the resident macrophages of the central nervous system (CNS). Their phagocytic activity is central during brain development and homeostasis-and in a plethora of brain pathologies. However, little is known about the composition, dynamics, and function of human microglial phagosomes under homeostatic and pathological conditions. Here, we developed a method for rapid isolation of pure and intact phagosomes from human pluripotent stem cell-derived microglia under various in vitro conditions, and from human brain biopsies, for unbiased multiomic analysis. Phagosome profiling revealed that microglial phagosomes were equipped to sense minute changes in their environment and were highly dynamic. We detected proteins involved in synapse homeostasis, or implicated in brain pathologies, and identified the phagosome as the site where quinolinic acid was stored and metabolized for de novo nicotinamide adenine dinucleotide (NAD+) generation in the cytoplasm. Our findings highlight the central role of phagosomes in microglial functioning in the healthy and diseased brain.
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Affiliation(s)
- Emile Wogram
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Felix Sümpelmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Eshaan Rawat
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | | | - Dongdong Fu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brandyn Braswell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Andrew Khalil
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; The Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA; Harvard John A. Paulson School of Engineering and Applied Sciences, Boston, MA 02134, USA
| | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Stefan Tholen
- Institute of Surgical Pathology, Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Medical Center, University of Freiburg, 79106 Freiburg, Germany
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Angelika S Rambold
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Oliver Schnell
- Department of Neurosurgery, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Jürgen Beck
- Department of Neurosurgery, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies and Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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3
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Li CM, Kang J, Baek J, Kim Y, Park H, Jung YK. Cytosolic FKBPL and ER-resident CKAP4 co-regulates ER-phagy and protein secretion. Nat Commun 2024; 15:7886. [PMID: 39251576 PMCID: PMC11383940 DOI: 10.1038/s41467-024-52188-7] [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: 05/26/2022] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
Endoplasmic reticulum quality control is crucial for maintaining cellular homeostasis and adapting to stress conditions. Although several ER-phagy receptors have been identified, the collaboration between cytosolic and ER-resident factors in ER fragmentation and ER-phagy regulation remains unclear. Here, we perform a phenotype-based gain-of-function screen and identify a cytosolic protein, FKBPL, functioning as an ER-phagy regulator. Overexpression of FKBPL triggers ER fragmentation and ER-phagy. FKBPL has multiple protein binding domains, can self-associate and might act as a scaffold connecting CKAP4 and LC3/GABARAPs. CKAP4 serves as a bridge between FKBPL and ER-phagy cargo. ER-phagy-inducing conditions increase FKBPL-CKAP4 interaction followed by FKBPL oligomerization at the ER, leading to ER-phagy. In addition, FKBPL-CKAP4 deficiency leads to Golgi disassembly and lysosome impairment, and an increase in ER-derived secretory vesicles and enhances cytosolic protein secretion via microvesicle shedding. Taken together, FKBPL with the aid of CKAP4 induces ER fragmentation and ER-phagy, and FKBPL-CKAP4 deficiency facilitates protein secretion.
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Affiliation(s)
- Cathena Meiling Li
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Jaemin Kang
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Jongyeon Baek
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Youbin Kim
- Interdisciplinary Program in Neuroscience, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Heemin Park
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Yong-Keun Jung
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul, Korea.
- Interdisciplinary Program in Neuroscience, Seoul National University, Gwanak-gu, Seoul, Korea.
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4
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Huang KT, Aye Y. Toward decoding spatiotemporal signaling activities of reactive immunometabolites with precision immuno-chemical biology tools. Commun Chem 2024; 7:195. [PMID: 39223329 PMCID: PMC11369232 DOI: 10.1038/s42004-024-01282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Immune-cell reprogramming driven by mitochondria-derived reactive electrophilic immunometabolites (mt-REMs-e.g., fumarate, itaconate) is an emerging phenomenon of major biomedical importance. Despite their localized production, mt-REMs elicit significantly large local and global footprints within and across cells, through mechanisms involving electrophile signaling. Burgeoning efforts are being put into profiling mt-REMs' potential protein-targets and phenotypic mapping of their multifaceted inflammatory behaviors. Yet, precision indexing of mt-REMs' first-responders with spatiotemporal intelligence and locale-specific function assignments remain elusive. Highlighting the latest advances and overarching challenges, this perspective aims to stimulate thoughts and spur interdisciplinary innovations to address these unmet chemical-biotechnological needs at therapeutic immuno-signaling frontiers.
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Affiliation(s)
- Kuan-Ting Huang
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- University of Oxford, Oxford, UK.
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5
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Park S, Wang X, Mo Y, Zhang S, Li X, Fong KC, Yu C, Tran AA, Scipioni L, Dai Z, Huang X, Huang L, Shi X. Proximity labeling expansion microscopy (PL-ExM) evaluates interactome labeling techniques. J Mater Chem B 2024; 12:8335-8348. [PMID: 39105364 DOI: 10.1039/d4tb00516c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Understanding protein-protein interactions (PPIs) through proximity labeling has revolutionized our comprehension of cellular mechanisms and pathology. Various proximity labeling techniques, such as HRP, APEX, BioID, TurboID, and μMap, have been widely used to biotinylate PPIs or organelles for proteomic profiling. However, the variability in labeling precision and efficiency of these techniques often results in limited reproducibility in proteomic detection. We address this persistent challenge by introducing proximity labeling expansion microscopy (PL-ExM), a super-resolution imaging technique that combines expansion microscopy with proximity labeling techniques. PL-ExM enabled up to 17 nm resolution with microscopes widely available, providing visual comparison of the labeling precision, efficiency, and false positives of different proximity labeling methods. Our mass spectrometry proteomic results confirmed that PL-ExM imaging is reliable in guiding the selection of proximity labeling techniques and interpreting the proteomic results with new spatial information.
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Affiliation(s)
- Sohyeon Park
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
| | - Xiaorong Wang
- Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Yajin Mo
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
| | - Sicheng Zhang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katie C Fong
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Clinton Yu
- Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Arthur A Tran
- Cardiovascular Research Institute, School of Medicine, University of California, San Francisco, San Francisco 94143, USA
| | - Lorenzo Scipioni
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Zhipeng Dai
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xiao Huang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA
| | - Lan Huang
- Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Xiaoyu Shi
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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6
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Xu J, Pickard JM, Núñez G. FDA-approved disulfiram inhibits the NLRP3 inflammasome by regulating NLRP3 palmitoylation. Cell Rep 2024; 43:114609. [PMID: 39116210 PMCID: PMC11398858 DOI: 10.1016/j.celrep.2024.114609] [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: 03/22/2024] [Revised: 06/23/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
The NLRP3 inflammasome is dysregulated in autoinflammatory disorders caused by inherited mutations and contributes to the pathogenesis of several chronic inflammatory diseases. In this study, we discovered that disulfiram, a safe US Food and Drug Administration (FDA)-approved drug, specifically inhibits the NLRP3 inflammasome but not the NLRC4 or AIM2 inflammasomes. Disulfiram suppresses caspase-1 activation, ASC speck formation, and pyroptosis induced by several stimuli that activate NLRP3. Mechanistically, NLRP3 is palmitoylated at cysteine 126, a modification required for its localization to the trans-Golgi network and inflammasome activation, which was inhibited by disulfiram. Administration of disulfiram to animals inhibited the NLRP3, but not NLRC4, inflammasome in vivo. Our study uncovers a mechanism by which disulfiram targets NLRP3 and provides a rationale for using a safe FDA-approved drug for the treatment of NLRP3-associated inflammatory diseases.
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Affiliation(s)
- Jie Xu
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Joseph M Pickard
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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7
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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8
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Guan J, Tang L, Wang Y, Fu M, Xia T, Zheng K, Sabi MM, Cong H, Wang J, Zhou C, Zhou H, Weiss LM, Qu H, Han B. Microsporidian EnP1 alters host cell H2B monoubiquitination and prevents ferroptosis facilitating microsporidia survival. Proc Natl Acad Sci U S A 2024; 121:e2400657121. [PMID: 39141344 PMCID: PMC11348272 DOI: 10.1073/pnas.2400657121] [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: 01/17/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024] Open
Abstract
Microsporidia are intracellular eukaryotic pathogens that pose a substantial threat to immunocompromised hosts. The way these pathogens manipulate host cells during infection remains poorly understood. Using a proximity biotinylation strategy we established that microsporidian EnP1 is a nucleus-targeted effector that modifies the host cell environment. EnP1's translocation to the host nucleus is meditated by nuclear localization signals (NLSs). In the nucleus, EnP1 interacts with host histone H2B. This interaction disrupts H2B monoubiquitination (H2Bub), subsequently impacting p53 expression. Crucially, this inhibition of p53 weakens its control over the downstream target gene SLC7A11, enhancing the host cell's resilience against ferroptosis during microsporidian infection. This favorable condition promotes the proliferation of microsporidia within the host cell. These findings shed light on the molecular mechanisms by which microsporidia modify their host cells to facilitate their survival.
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Affiliation(s)
- Jingyu Guan
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Liyuan Tang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Yongliang Wang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Ming Fu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Tian Xia
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Kai Zheng
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Musa Makongoro Sabi
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Hua Cong
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Juncheng Wang
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Chunxue Zhou
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Huaiyu Zhou
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Louis M. Weiss
- Department of Pathology, Albert Einstein College of Medicine, New York, NY10461
| | - Hongnan Qu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Bing Han
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
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9
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Stockhammer A, Spalt C, Klemt A, Benz LS, Harel S, Natalia V, Wiench L, Freund C, Kuropka B, Bottanelli F. When less is more - a fast TurboID knock-in approach for high-sensitivity endogenous interactome mapping. J Cell Sci 2024; 137:jcs261952. [PMID: 39056144 PMCID: PMC11385326 DOI: 10.1242/jcs.261952] [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: 01/11/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
In recent years, proximity labeling has established itself as an unbiased and powerful approach to map the interactome of specific proteins. Although physiological expression of labeling enzymes is beneficial for the mapping of interactors, generation of the desired cell lines remains time-consuming and challenging. Using our established pipeline for rapid generation of C- and N-terminal CRISPR-Cas9 knock-ins (KIs) based on antibiotic selection, we were able to compare the performance of commonly used labeling enzymes when endogenously expressed. Endogenous tagging of the µ subunit of the adaptor protein (AP)-1 complex with TurboID allowed identification of known interactors and cargo proteins that simple overexpression of a labeling enzyme fusion protein could not reveal. We used the KI strategy to compare the interactome of the different AP complexes and clathrin and were able to assemble lists of potential interactors and cargo proteins that are specific for each sorting pathway. Our approach greatly simplifies the execution of proximity labeling experiments for proteins in their native cellular environment and allows going from CRISPR transfection to mass spectrometry analysis and interactome data in just over a month.
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Affiliation(s)
- Alexander Stockhammer
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Carissa Spalt
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Antonia Klemt
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Laila S Benz
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Shelly Harel
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Vini Natalia
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Lukas Wiench
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Benno Kuropka
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Francesca Bottanelli
- Membrane Trafficking Laboratory, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
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10
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Lin Z, Liu D, Xu Y, Wang M, Yu Y, Diener AC, Liu KH. Pupylation-based proximity-tagging of FERONIA-interacting proteins in Arabidopsis. Mol Cell Proteomics 2024:100828. [PMID: 39147029 DOI: 10.1016/j.mcpro.2024.100828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/11/2024] [Accepted: 08/07/2024] [Indexed: 08/17/2024] Open
Abstract
The plasma membrane-localized receptor kinase FERONIA (FER) plays critical roles in a remarkable variety of biological processes throughout the life cycle of Arabidopsis thaliana. Revealing the molecular connections of FER that underlie these processes starts with identifying the proteins that interact with FER. We applied pupylation-based interaction tagging (PUP-IT) to survey cellular proteins in proximity to FER, encompassing weak and transient interactions that can be difficult to capture for membrane proteins. We reproducibly identified 581, 115, and 736 specific FER-interacting protein candidates in protoplasts, seedlings, and flowers, respectively. We also confirmed fourteen previously characterized FER-interacting proteins. Protoplast transient gene expression expedited the testing of new gene constructs for PUP-IT analyses and the validation of candidate proteins. We verified the proximity labeling of five selected candidates that were not previously characterized as FER-interacting proteins. The PUP-IT method could be a valuable tool to survey and validate protein-protein interactions for targets of interest in diverse subcellular compartments in plants.
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Affiliation(s)
- Zhuoran Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Di Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Yifan Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Mengyang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - YongQi Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Andrew C Diener
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Kun-Hsiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China; Institute of Future Agriculture, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China; Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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11
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Mukhopadhyay U, Levantovsky S, Carusone TM, Gharbi S, Stein F, Behrends C, Bhogaraju S. A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates. SCIENCE ADVANCES 2024; 10:eadp3000. [PMID: 39121224 PMCID: PMC11313854 DOI: 10.1126/sciadv.adp3000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/03/2024] [Indexed: 08/11/2024]
Abstract
Over 600 E3 ligases in humans execute ubiquitination of specific target proteins in a spatiotemporal manner to elicit desired signaling effects. Here, we developed a ubiquitin-specific proximity-based labeling method to selectively biotinylate substrates of a given ubiquitin ligase. By fusing the biotin ligase BirA and an Avi-tag variant to the candidate E3 ligase and ubiquitin, respectively, we were able to specifically enrich bona fide substrates of a ligase using a one-step streptavidin pulldown under denaturing conditions. We applied our method, which we named Ub-POD, to the really interesting new gene (RING) E3 ligase RAD18 and identified proliferating cell nuclear antigen and several other critical players in the DNA damage repair pathway. Furthermore, we successfully applied Ub-POD to the RING ubiquitin ligase tumor necrosis factor receptor-associated factor 6 and a U-box-type E3 ubiquitin ligase carboxyl terminus of Hsc70-interacting protein. We anticipate that our method could be widely adapted to all classes of ubiquitin ligases to identify substrates.
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Affiliation(s)
- Urbi Mukhopadhyay
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Sophie Levantovsky
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Teresa Maria Carusone
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Sarah Gharbi
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sagar Bhogaraju
- European Molecular Biology Laboratory, 71 avenue des Martyrs, 38042 Grenoble, France
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12
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Deng H, Jia G, Li P, Tang Y, Zhao L, Yang Q, Zhao J, Wang J, Tu Y, Yong X, Zhang S, Mo X, Billadeau DD, Su Z, Jia D. The WDR11 complex is a receptor for acidic-cluster-containing cargo proteins. Cell 2024; 187:4272-4288.e20. [PMID: 39013469 PMCID: PMC11316641 DOI: 10.1016/j.cell.2024.06.024] [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: 12/11/2023] [Revised: 05/06/2024] [Accepted: 06/18/2024] [Indexed: 07/18/2024]
Abstract
Vesicle trafficking is a fundamental process that allows for the sorting and transport of specific proteins (i.e., "cargoes") to different compartments of eukaryotic cells. Cargo recognition primarily occurs through coats and the associated proteins at the donor membrane. However, it remains unclear whether cargoes can also be selected at other stages of vesicle trafficking to further enhance the fidelity of the process. The WDR11-FAM91A1 complex functions downstream of the clathrin-associated AP-1 complex to facilitate protein transport from endosomes to the TGN. Here, we report the cryo-EM structure of human WDR11-FAM91A1 complex. WDR11 directly and specifically recognizes a subset of acidic clusters, which we term super acidic clusters (SACs). WDR11 complex assembly and its binding to SAC-containing proteins are indispensable for the trafficking of SAC-containing proteins and proper neuronal development in zebrafish. Our studies thus uncover that cargo proteins could be recognized in a sequence-specific manner downstream of a protein coat.
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Affiliation(s)
- Huaqing Deng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guowen Jia
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610044, China
| | - Ping Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yingying Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lin Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Qin Yang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jia Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jinrui Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yingfeng Tu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Xianming Mo
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhaoming Su
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610044, China.
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China.
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13
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Rondón-Ortiz AN, Zhang L, Ash PEA, Basu A, Puri S, van der Spek SJF, Wang Z, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. J Biol Chem 2024; 300:107621. [PMID: 39098523 PMCID: PMC11401034 DOI: 10.1016/j.jbc.2024.107621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/30/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Sequestosome1 (SQSTM1) is an autophagy receptor that mediates the degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA, and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and the relationship between the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.
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Affiliation(s)
- Alejandro N Rondón-Ortiz
- Department of Biology, Boston University, Boston, Massachusetts, USA; Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Departments of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA
| | - Lushuang Zhang
- Departments of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA
| | - Peter E A Ash
- Departments of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University, Boston, Massachusetts, USA; Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, Oregon, USA
| | - Sambhavi Puri
- Departments of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA
| | | | - Zihan Wang
- Departments of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA
| | - Luke Dorrian
- Departments of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University, Boston, Massachusetts, USA; Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, Oregon, USA.
| | - Benjamin Wolozin
- Departments of Anatomy & Neurobiology, Boston University, Boston, Massachusetts, USA; Center for Systems Neuroscience, Boston University, Boston, Massachusetts, USA; Center for Neurophotonics, Boston University, Boston, Massachusetts, USA; Department of Neurology, Boston University, Boston, Massachusetts, USA; Department of Pharmacology, Physiology and Biophysics, Boston University, Boston, Massachusetts, USA.
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14
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Sun W, Huang A, Wen S, Yang R, Liu X. Temporal Assessment of Protein Stability in Dried Blood Spots. J Proteome Res 2024; 23:3585-3597. [PMID: 38950347 DOI: 10.1021/acs.jproteome.4c00233] [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: 07/03/2024]
Abstract
The use of protein biomarkers in blood for clinical settings is limited by the cost and accessibility of traditional venipuncture sampling. The dried blood spot (DBS) technique offers a less invasive and more accessible alternative. However, protein stability in DBS has not been well evaluated. Herein, we deployed a quantitative LC-MS/MS system to construct proteomic atlases of whole blood, DBSs, plasma, and blood cells. Approximately 4% of detected proteins' abundance was significantly altered during blood drying into blood spots, with overwhelming disturbances in cytoplasmic fraction. We also reported a novel finding suggesting a decrease in the level of membrane/cytoskeletal proteins (SLC4A1, RHAG, DSC1, DSP, and JUP) and an increase in the level of proteins (ATG3, SEC14L4, and NRBP1) related to intracellular trafficking. Furthermore, we identified 19 temporally dynamic proteins in DBS samples stored at room temperature for up to 6 months. There were three declined cytoskeleton-related proteins (RDX, SH3BGRL3, and MYH9) and four elevated proteins (XPO7, RAN, SLC2A1, and SLC29A1) involved in cytoplasmic transport as representatives. The instability was governed predominantly by hydrophilic proteins and enhanced significantly with an increasing storage time. Our analyses provide comprehensive knowledge of both short- and long-term storage stability of DBS proteins, forming the foundation for the widespread use of DBS in clinical proteomics and other analytical applications.
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Affiliation(s)
- Weifen Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
| | - Ao Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, Jiangsu Province, China
| | - Shubo Wen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, Jiangsu Province, China
| | - Ruicong Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, Yunnan Province, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science Ministry of Justice, Shanghai 200063, China
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15
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Pirayeshfard L, Luo S, Githaka JM, Saini A, Touret N, Goping IS, Julien O. Comparing the BAD Protein Interactomes in 2D and 3D Cell Culture Using Proximity Labeling. J Proteome Res 2024; 23:3433-3443. [PMID: 38959414 PMCID: PMC11302415 DOI: 10.1021/acs.jproteome.4c00111] [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: 02/16/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Protein-protein interaction studies using proximity labeling techniques, such as biotin ligase-based BioID, have become integral in understanding cellular processes. Most studies utilize conventional 2D cell culture systems, potentially missing important differences in protein behavior found in 3D tissues. In this study, we investigated the protein-protein interactions of a protein, Bcl-2 Agonist of cell death (BAD), and compared conventional 2D culture conditions to a 3D system, wherein cells were embedded within a 3D extracellular matrix (ECM) mimic. Using BAD fused to the engineered biotin ligase miniTurbo (BirA*), we identified both overlapping and distinct BAD interactomes under 2D and 3D conditions. The known BAD binding proteins 14-3-3 isoforms and Bcl-XL interacted with BAD in both 2D and 3D. Of the 131 BAD-interactors identified, 56% were specific to 2D, 14% were specific to 3D, and 30% were common to both conditions. Interaction network analysis demonstrated differential associations between 2D and 3D interactomes, emphasizing the impact of the culture conditions on protein interactions. The 2D-3D overlap interactome encapsulated the apoptotic program, which is a well-known role of BAD. The 3D unique pathways were enriched in ECM signaling, suggestive of hitherto unknown functions for BAD. Thus, exploring protein-protein interactions in 3D provides novel clues into cell behavior. This exciting approach has the potential to bridge the knowledge gap between tractable 2D cell culture and organoid-like 3D systems.
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Affiliation(s)
- Leila Pirayeshfard
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Shu Luo
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | | - Arashdeep Saini
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Nicolas Touret
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ing Swie Goping
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Department
of Oncology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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16
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Bowen CA, Nguyen HM, Lin Y, Bagchi P, Natu A, Espinosa-Garcia C, Werner E, Kumari R, Brandelli AD, Kumar P, Tobin BR, Wood L, Faundez V, Wulff H, Seyfried NT, Rangaraju S. Proximity Labeling Proteomics Reveals Kv1.3 Potassium Channel Immune Interactors in Microglia. Mol Cell Proteomics 2024; 23:100809. [PMID: 38936775 DOI: 10.1016/j.mcpro.2024.100809] [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: 03/09/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024] Open
Abstract
Microglia are resident immune cells of the brain and regulate its inflammatory state. In neurodegenerative diseases, microglia transition from a homeostatic state to a state referred to as disease-associated microglia (DAM). DAM express higher levels of proinflammatory signaling molecules, like STAT1 and TLR2, and show transitions in mitochondrial activity toward a more glycolytic response. Inhibition of Kv1.3 decreases the proinflammatory signature of DAM, though how Kv1.3 influences the response is unknown. Our goal was to identify the potential proteins interacting with Kv1.3 during transition to DAM. We utilized TurboID, a biotin ligase, fused to Kv1.3 to evaluate potential interacting proteins with Kv1.3 via mass spectrometry in BV-2 microglia following TLR4-mediated activation. Electrophysiology, Western blotting, and flow cytometry were used to evaluate Kv1.3 channel presence and TurboID biotinylation activity. We hypothesized that Kv1.3 contains domain-specific interactors that vary during a TLR4-induced inflammatory response, some of which are dependent on the PDZ-binding domain on the C terminus. We determined that the N terminus of Kv1.3 is responsible for trafficking Kv1.3 to the cell surface and mitochondria (e.g., NUDC, TIMM50). Whereas, the C terminus interacts with immune signaling proteins in a lipopolysaccharide-induced inflammatory response (e.g., STAT1, TLR2, and C3). There are 70 proteins that rely on the C-terminal PDZ-binding domain to interact with Kv1.3 (e.g., ND3, Snx3, and Sun1). Furthermore, we used Kv1.3 blockade to verify functional coupling between Kv1.3 and interferon-mediated STAT1 activation. Overall, we highlight that the Kv1.3 potassium channel functions beyond conducting the outward flux of potassium ions in an inflammatory context and that Kv1.3 modulates the activity of key immune signaling proteins, such as STAT1 and C3.
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Affiliation(s)
- Christine A Bowen
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Hai M Nguyen
- Department of Pharmacology, University of California - Davis, Davis, California, USA
| | - Young Lin
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Pritha Bagchi
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Aditya Natu
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | | | - Erica Werner
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | - Rashmi Kumari
- School of Medicine, Yale University, New Haven, Connecticut, USA
| | | | - Prateek Kumar
- School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Brendan R Tobin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Levi Wood
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Enigneering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Victor Faundez
- Department of Cell Biology, Emory University, Atlanta, Georgia, USA
| | - Heike Wulff
- Department of Pharmacology, University of California - Davis, Davis, California, USA
| | - Nicholas T Seyfried
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Srikant Rangaraju
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; School of Medicine, Yale University, New Haven, Connecticut, USA.
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17
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Saulnier O, Zagozewski J, Liang L, Hendrikse LD, Layug P, Gordon V, Aldinger KA, Haldipur P, Borlase S, Coudière-Morrison L, Cai T, Martell E, Gonzales NM, Palidwor G, Porter CJ, Richard S, Sharif T, Millen KJ, Doble BW, Taylor MD, Werbowetski-Ogilvie TE. A group 3 medulloblastoma stem cell program is maintained by OTX2-mediated alternative splicing. Nat Cell Biol 2024; 26:1233-1246. [PMID: 39025928 PMCID: PMC11321995 DOI: 10.1038/s41556-024-01460-5] [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: 06/17/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
OTX2 is a transcription factor and known driver in medulloblastoma (MB), where it is amplified in a subset of tumours and overexpressed in most cases of group 3 and group 4 MB. Here we demonstrate a noncanonical role for OTX2 in group 3 MB alternative splicing. OTX2 associates with the large assembly of splicing regulators complex through protein-protein interactions and regulates a stem cell splicing program. OTX2 can directly or indirectly bind RNA and this may be partially independent of its DNA regulatory functions. OTX2 controls a pro-tumorigenic splicing program that is mirrored in human cerebellar rhombic lip origins. Among the OTX2-regulated differentially spliced genes, PPHLN1 is expressed in the most primitive rhombic lip stem cells, and targeting PPHLN1 splicing reduces tumour growth and enhances survival in vivo. These findings identify OTX2-mediated alternative splicing as a major determinant of cell fate decisions that drive group 3 MB progression.
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Affiliation(s)
- Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genomics and Development of Childhood Cancers, Institut Curie, PSL University, Paris, France
- INSERM U830, Cancer, Heterogeneity, Instability and Plasticity, Institut Curie, PSL University, Paris, France
- SIREDO Oncology Center, Institut Curie, Paris, France
| | - Jamie Zagozewski
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Lisa Liang
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Liam D Hendrikse
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Paul Layug
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Victor Gordon
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Stephanie Borlase
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ludivine Coudière-Morrison
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ting Cai
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
| | - Emma Martell
- Department of Pathology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Naomi M Gonzales
- Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Gareth Palidwor
- Ottawa Bioinformatics Core Facility, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Christopher J Porter
- Ottawa Bioinformatics Core Facility, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
| | - Tanveer Sharif
- Department of Pathology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Brad W Doble
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Texas Children's Hospital, Houston, TX, USA.
- Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
- Texas Children's Cancer and Hematology Center, Houston, TX, USA.
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA.
- Department of Neurosurgery, Texas Children's Hospital, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Tamra E Werbowetski-Ogilvie
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
- Texas Children's Hospital, Houston, TX, USA.
- Department of Pediatrics, Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Cancer and Hematology Center, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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18
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Liu Y, McGann CD, Krebs M, Perkins TA, Fields R, Camplisson CK, Nwizugbo DZ, Hsu C, Avanessian SC, Tsue AF, Kania EE, Shechner DM, Beliveau BJ, Schweppe DK. DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604987. [PMID: 39091817 PMCID: PMC11291153 DOI: 10.1101/2024.07.24.604987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The accuracy of crucial nuclear processes such as transcription, replication, and repair, depends on the local composition of chromatin and the regulatory proteins that reside there. Understanding these DNA-protein interactions at the level of specific genomic loci has remained challenging due to technical limitations. Here, we introduce a method termed "DNA O-MAP", which uses programmable peroxidase-conjugated oligonucleotide probes to biotinylate nearby proteins. We show that DNA O-MAP can be coupled with sample multiplexed quantitative proteomics and next-generation sequencing to quantify DNA-protein and DNA-DNA interactions at specific genomic loci.
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Affiliation(s)
- Yuzhen Liu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- These authors contributed equally: Yuzhen Liu, Christopher D. McGann
| | - Christopher D. McGann
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- These authors contributed equally: Yuzhen Liu, Christopher D. McGann
| | - Mary Krebs
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Thomas A. Perkins
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Conor K. Camplisson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - David Z. Nwizugbo
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Chris Hsu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Shayan C. Avanessian
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Ashley F. Tsue
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
| | - Evan E. Kania
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
| | - David M. Shechner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
| | - Brian J. Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
| | - Devin K. Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, USA
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19
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Tang L, Sabi MM, Fu M, Guan J, Wang Y, Xia T, Zheng K, Qu H, Han B. Host cell manipulation by microsporidia secreted effectors: Insights into intracellular pathogenesis. J Eukaryot Microbiol 2024:e13029. [PMID: 39030770 DOI: 10.1111/jeu.13029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 07/22/2024]
Abstract
Microsporidia are prolific producers of effector molecules, encompassing both proteins and nonproteinaceous effectors, such as toxins, small RNAs, and small peptides. These secreted effectors play a pivotal role in the pathogenicity of microsporidia, enabling them to subvert the host's innate immunity and co-opt metabolic pathways to fuel their own growth and proliferation. However, the genomes of microsporidia, despite falling within the size range of bacteria, exhibit significant reductions in both structural and physiological features, thereby affecting the repertoire of secretory effectors to varying extents. This review focuses on recent advances in understanding how microsporidia modulate host cells through the secretion of effectors, highlighting current challenges and proposed solutions in deciphering the complexities of microsporidial secretory effectors.
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Affiliation(s)
- Liyuan Tang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Musa Makongoro Sabi
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Ming Fu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Jingyu Guan
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Yongliang Wang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Tian Xia
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Kai Zheng
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
| | - Hongnan Qu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen, Guangdong, China
| | - Bing Han
- Department of Pathogenic Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China
- Shenzhen Research Institute, Shandong University, Shenzhen, Guangdong, China
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20
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Ortmann BM, Taylor CT, Rocha S. Hypoxia research, where to now? Trends Biochem Sci 2024; 49:573-582. [PMID: 38599898 DOI: 10.1016/j.tibs.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/01/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Investigating how cells and organisms sense and respond to O2 levels is essential to our understanding of physiology and pathology. This field has advanced considerably since the discovery of the major transcription factor family, hypoxia-inducible factor (HIF), and the enzymes that control its levels: prolyl hydroxylases (PHDs). However, with its expansion, new complexities have emerged. Herein we highlight three main areas where, in our opinion, the research community could direct some of their attention. These include non-transcriptional roles of HIFs, specificity and O2 sensitivity of 2-oxoglutarate-dependent dioxygenases (2-OGDDs), and new tools and methods to detect O2 concentrations in cells and organs. A greater understanding of these areas would answer big questions and help drive our knowledge of cellular responses to hypoxia forward.
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Affiliation(s)
- Brian M Ortmann
- Wolfson Childhood Cancer Research Centre, Newcastle University, Newcastle upon Tyne, UK.
| | - Cormac T Taylor
- School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland.
| | - Sonia Rocha
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
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21
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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 PMCID: PMC11381016 DOI: 10.1152/physrev.00026.2023] [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: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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22
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Kim JW, Yong AJH, Aisenberg EE, Lobel JH, Wang W, Dawson TM, Dawson VL, Gao R, Jan YN, Bateup HS, Ingolia NT. Molecular recording of calcium signals via calcium-dependent proximity labeling. Nat Chem Biol 2024; 20:894-905. [PMID: 38658655 DOI: 10.1038/s41589-024-01603-7] [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: 04/13/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024]
Abstract
Calcium ions serve as key intracellular signals. Local, transient increases in calcium concentrations can activate calcium sensor proteins that in turn trigger downstream effectors. In neurons, calcium transients play a central role in regulating neurotransmitter release and synaptic plasticity. However, it is challenging to capture the molecular events associated with these localized and ephemeral calcium signals. Here we present an engineered biotin ligase that generates permanent molecular traces in a calcium-dependent manner. The enzyme, calcium-dependent BioID (Cal-ID), biotinylates nearby proteins within minutes in response to elevated local calcium levels. The biotinylated proteins can be identified via mass spectrometry and visualized using microscopy. In neurons, Cal-ID labeling is triggered by neuronal activity, leading to prominent protein biotinylation that enables transcription-independent activity labeling in the brain. In summary, Cal-ID produces a biochemical record of calcium signals and neuronal activity with high spatial resolution and molecular specificity.
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Affiliation(s)
- J Wren Kim
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Adeline J H Yong
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Erin E Aisenberg
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
| | - Joseph H Lobel
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
| | - Wei Wang
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Ted M Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruixuan Gao
- Department of Chemistry at the University of Illinois, Chicago, Chicago, IL, USA
| | - Yuh Nung Jan
- Department of Physiology at the University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA, USA
| | - Helen S Bateup
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute at the University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology at the University of California, Berkeley, Berkeley, CA, USA.
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23
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Ortiz ANR, Zhang L, Ash PE, Basu A, Puri S, van der Spek SJ, Wang Z, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571324. [PMID: 38168279 PMCID: PMC10760047 DOI: 10.1101/2023.12.12.571324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and of the relationship of the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.
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Affiliation(s)
- Alejandro N. Rondón Ortiz
- Department of Biology, Boston University, Boston, MA 02215, USA
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Lushuang Zhang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Peter E.A. Ash
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Sambhavi Puri
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | | | - Zihan Wang
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Luke Dorrian
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02215, USA
- Department of Biochemistry, Boston University, Boston, MA 02115, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Benjamin Wolozin
- Departments of Anatomy & Neurobiology, Boston University, Boston, MA 02215, USA
- Center for Systems Neuroscience, Boston University, Boston, MA 02115, USA
- Center for Neurophotonics, Boston University, Boston, MA 02115, USA
- Department of Neurology, Boston University, Boston, MA 02115, USA
- Department of Pharmacology, Physiology and Biophysics
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24
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Liu H, Huang R, Zhuo Z, Zhang X, Wu L, Guo Z, Wen F, An L, Yuan H, Zhang Y, Xu Y. Activation of kappa opioid receptor suppresses post-traumatic osteoarthritis via sequestering STAT3 on the plasma membrane. Cell Commun Signal 2024; 22:335. [PMID: 38890746 PMCID: PMC11186255 DOI: 10.1186/s12964-024-01709-4] [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: 01/31/2024] [Accepted: 06/09/2024] [Indexed: 06/20/2024] Open
Abstract
OBJECTIVE Kappa opioid receptor (KOR) signaling is involved in joint development and inflammation in Osteoarthritis (OA), while the biochemical mechanism remains unclarified. This study aims to investigate downstream molecular events of KOR activation, to provide novel perspectives in OA pathology. METHODS U50,488H, a selective KOR agonist, was intra-articularly injected in mice upon destabilization of the medial meniscus (DMM) as OA models, with PBS injection as control. The behavioral and histological evaluation was assessed by hot plate test and red solid green staining, respectively. Alterations in mRNA and protein expression were assessed by RNA-seq, RT-qPCR, immunohistochemistry and western blotting (WB) in chondrocytes treated with TNF-α or TNF-α + U50,488H. Proteins interacted with KOR were explored using proximity labeling followed by mass spectrometry and then testified by co-immunoprecipitation (Co-IP) assay and immunofluorescence (IF). RESULTS OA-induced pain was reduced and cartilage degeneration was alleviated upon KOR activation in DMM mice. In chondrocytes, activation of KOR reversed the upregulation of MMPs, IL-6, IL-1β and phosphorylated(p-) STAT3, stimulated by TNF-α, while the expression of NF-κB, MAPKs and AKT signaling weren't reversed. RNA-seq and IF results presented that KOR activation evidently reduced STAT3 nuclear translocation in chondrocytes upon TNF-α stimuli. The reduction may be resulted from the binding of KOR and STAT3 in the plasma membrane, revealed by proximity labeling and Co-IP results. CONCLUSIONS KOR activation protects cartilage from OA, and this protective effect is mainly exerted via sequestering STAT3 on the plasma membrane, resulting in inactivation of STAT3-dependent immune responses which otherwise contributes to OA.
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Affiliation(s)
- Haixia Liu
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Renhuan Huang
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ziang Zhuo
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinru Zhang
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ling Wu
- iView Therapeutics, Inc., Cranbury, NJ, USA
| | - Zhen Guo
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fuping Wen
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Liwei An
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hang Yuan
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Yiming Zhang
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Yuanzhi Xu
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
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25
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Xie Y, Cao J, Gan S, Xu L, Zhang D, Qian S, Xu F, Ding Q, Schoggins JW, Fan W. TRIM32 inhibits Venezuelan Equine Encephalitis Virus Infection by targeting a late step in viral entry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597282. [PMID: 38895352 PMCID: PMC11185716 DOI: 10.1101/2024.06.04.597282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Alphaviruses are mosquito borne RNA viruses that are a reemerging public health threat. Alphaviruses have a broad host range, and can cause diverse disease outcomes like arthritis, and encephalitis. The host ubiquitin proteasome system (UPS) plays critical roles in regulating cellular processes to control the infections with various viruses, including alphaviruses. Previous studies suggest alphaviruses hijack UPS for virus infection, but the molecular mechanisms remain poorly characterized. In addition, whether certain E3 ubiquitin ligases or deubiquitinases act as alphavirus restriction factors remains poorly understood. Here, we employed a cDNA expression screen to identify E3 ubiquitin ligase TRIM32 as a novel intrinsic restriction factor against alphavirus infection, including VEEV-TC83, SINV, and ONNV. Ectopic expression of TRIM32 reduces alphavirus infection, whereas depletion of TRIM32 with CRISPR-Cas9 increases infection. We demonstrate that TRIM32 inhibits alphaviruses through a mechanism that is independent of the TRIM32-STING-IFN axis. Combining reverse genetics and biochemical assays, we found that TRIM32 interferes with genome translation after membrane fusion, prior to replication of the incoming viral genome. Furthermore, our data indicate that the monoubiquitination of TRIM32 is important for its antiviral activity. Notably, we also show two TRIM32 pathogenic mutants R394H and D487N, related to Limb-girdle muscular dystrophy (LGMD), have a loss of antiviral activity against VEEV-TC83. Collectively, these results reveal that TRIM32 acts as a novel intrinsic restriction factor suppressing alphavirus infection and provides insights into the interaction between alphaviruses and the host UPS.
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Affiliation(s)
- Yifan Xie
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jie Cao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shuyi Gan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lingdong Xu
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Dongjie Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Suhong Qian
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, China
| | - Qiang Ding
- School of Medical Sciences, Tsinghua University, Beijing, China
| | - John W. Schoggins
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenchun Fan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
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26
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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27
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Armingol E, Baghdassarian HM, Lewis NE. The diversification of methods for studying cell-cell interactions and communication. Nat Rev Genet 2024; 25:381-400. [PMID: 38238518 PMCID: PMC11139546 DOI: 10.1038/s41576-023-00685-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 05/20/2024]
Abstract
No cell lives in a vacuum, and the molecular interactions between cells define most phenotypes. Transcriptomics provides rich information to infer cell-cell interactions and communication, thus accelerating the discovery of the roles of cells within their communities. Such research relies heavily on algorithms that infer which cells are interacting and the ligands and receptors involved. Specific pressures on different research niches are driving the evolution of next-generation computational tools, enabling new conceptual opportunities and technological advances. More sophisticated algorithms now account for the heterogeneity and spatial organization of cells, multiple ligand types and intracellular signalling events, and enable the use of larger and more complex datasets, including single-cell and spatial transcriptomics. Similarly, new high-throughput experimental methods are increasing the number and resolution of interactions that can be analysed simultaneously. Here, we explore recent progress in cell-cell interaction research and highlight the diversification of the next generation of tools, which have yielded a rich ecosystem of tools for different applications and are enabling invaluable discoveries.
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Affiliation(s)
- Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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28
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Enström A, Carlsson R, Buizza C, Lewi M, Paul G. Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular in Vitro Spheroid Model. Mol Cell Proteomics 2024; 23:100782. [PMID: 38705386 PMCID: PMC11176767 DOI: 10.1016/j.mcpro.2024.100782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 04/09/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024] Open
Abstract
Cellular communication within the brain is imperative for maintaining homeostasis and mounting effective responses to pathological triggers like hypoxia. However, a comprehensive understanding of the precise composition and dynamic release of secreted molecules has remained elusive, confined primarily to investigations using isolated monocultures. To overcome these limitations, we utilized the potential of TurboID, a non-toxic biotin ligation enzyme, to capture and enrich secreted proteins specifically originating from human brain pericytes in spheroid cocultures with human endothelial cells and astrocytes. This approach allowed us to characterize the pericyte secretome within a more physiologically relevant multicellular setting encompassing the constituents of the blood-brain barrier. Through a combination of mass spectrometry and multiplex immunoassays, we identified a wide spectrum of different secreted proteins by pericytes. Our findings demonstrate that the pericytes secretome is profoundly shaped by their intercellular communication with other blood-brain barrier-residing cells. Moreover, we identified substantial differences in the secretory profiles between hypoxic and normoxic pericytes. Mass spectrometry analysis showed that hypoxic pericytes in coculture increase their release of signals related to protein secretion, mTOR signaling, and the complement system, while hypoxic pericytes in monocultures showed an upregulation in proliferative pathways including G2M checkpoints, E2F-, and Myc-targets. In addition, hypoxic pericytes show an upregulation of proangiogenic proteins such as VEGFA but display downregulation of canonical proinflammatory cytokines such as CXCL1, MCP-1, and CXCL6. Understanding the specific composition of secreted proteins in the multicellular brain microvasculature is crucial for advancing our knowledge of brain homeostasis and the mechanisms underlying pathology. This study has implications for the identification of targeted therapeutic strategies aimed at modulating microvascular signaling in brain pathologies associated with hypoxia.
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Affiliation(s)
- Andreas Enström
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Robert Carlsson
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Carolina Buizza
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Marvel Lewi
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Gesine Paul
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden; Department of Neurology, Scania University Hospital, Lund, Sweden; Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
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29
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Zhu Q, Geng D, Li J, Zhang J, Sun H, Fan Z, He J, Hao N, Tian Y, Wen L, Li T, Qin W, Chu X, Wang Y, Yi W. A Computational and Chemical Design Strategy for Manipulating Glycan-Protein Recognition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308522. [PMID: 38582526 PMCID: PMC11199974 DOI: 10.1002/advs.202308522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/23/2024] [Indexed: 04/08/2024]
Abstract
Glycans are complex biomolecules that encode rich information and regulate various biological processes, such as fertilization, host-pathogen binding, and immune recognition, through interactions with glycan-binding proteins. A key driving force for glycan-protein recognition is the interaction between the π electron density of aromatic amino acid side chains and polarized C─H groups of the pyranose (termed the CH-π interaction). However, the relatively weak binding affinity between glycans and proteins has hindered the application of glycan detection and imaging. Here, computational modeling and molecular dynamics simulations are employed to design a chemical strategy that enhances the CH-π interaction between glycans and proteins by genetically incorporating electron-rich tryptophan derivatives into a lectin PhoSL, which specifically recognizes core fucosylated N-linked glycans. This significantly enhances the binding affinity of PhoSL with the core fucose ligand and enables sensitive detection and imaging of core fucosylated glycans in vitro and in xenograft tumors in mice. Further, the study showed that this strategy is applicable to improve the binding affinity of GafD lectin for N-acetylglucosamine-containing glycans. The approach thus provides a general and effective way to manipulate glycan-protein recognition for glycoscience applications.
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Affiliation(s)
- Qiang Zhu
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Didi Geng
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Jingchao Li
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Jinqiu Zhang
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Haofan Sun
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Zhiya Fan
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Jiahui He
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Ninghui Hao
- The Provincial International Science and Technology Cooperation Base on Engineering BiologyShanghai Institute for Advanced StudyInstitute of Quantitative BiologyInternational Campus of Zhejiang UniversityHaining314499China
| | - Yinping Tian
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Liuqing Wen
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Tiehai Li
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Weijie Qin
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Xiakun Chu
- Advanced Materials ThrustFunction HubThe Hong Kong University of Science and TechnologyGuangzhou511400China
| | - Yong Wang
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
- The Provincial International Science and Technology Cooperation Base on Engineering BiologyShanghai Institute for Advanced StudyInstitute of Quantitative BiologyInternational Campus of Zhejiang UniversityHaining314499China
| | - Wen Yi
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
- Cancer CentreZhejiang UniversityHangzhou310012China
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30
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Nguyen DTM, Koppers M, Farías GG. Endoplasmic reticulum - condensate interactions in protein synthesis and secretion. Curr Opin Cell Biol 2024; 88:102357. [PMID: 38626704 DOI: 10.1016/j.ceb.2024.102357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/18/2024]
Abstract
In the past decade, a growing amount of evidence has demonstrated that organelles do not act autonomously and independently but rather communicate with each other to coordinate different processes for proper cellular function. With a highly extended network throughout the cell, the endoplasmic reticulum (ER) plays a central role in interorganelle communication through membrane contact sites. Here, we highlight recent evidence indicating that the ER also forms contacts with membrane-less organelles. These interactions contribute to the dynamic assembly and disassembly of condensates and controlled protein secretion. Additionally, emerging evidence suggests their involvement in mRNA localization and localized translation. We further explore exciting future directions of this emerging theme in the organelle contact site field.
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Affiliation(s)
- Dan T M Nguyen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Max Koppers
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Ginny G Farías
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
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31
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Goyal P, Tao AJ, Mumby EJ, English JG, Ferguson FM. Measuring Ligand-bound Protein Complexes with Proximity Labeling: A Practical Guide. Chembiochem 2024; 25:e202400073. [PMID: 38457625 DOI: 10.1002/cbic.202400073] [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: 01/29/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
Identifying the drug-target interactome of small molecule therapeutics is essential for understanding the full pharmacological effects of a compound. These therapies often induce changes within the cellular proteome, leading to unexpected consequences such as changes in the targets complexation state or off-target interactions between the compound and additional proteins. Currently, unbiased target-ID approaches are being used to embark on this task. Here we provide an overview of the strengths and limitations of these methods, and a practical step-by-step protocol for using the BioTAC system to assist with drug target and interactome ID.
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Affiliation(s)
- Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
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32
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Bae J, Kim J, Choi J, Lee H, Koh M. Split Proteins and Reassembly Modules for Biological Applications. Chembiochem 2024; 25:e202400123. [PMID: 38530024 DOI: 10.1002/cbic.202400123] [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: 02/08/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation. This review offers a comprehensive perspective on the recent evolution of split systems in biological research.
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Affiliation(s)
- Jieun Bae
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Jongdoo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
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33
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Irala D, Wang S, Sakers K, Nagendren L, Ulloa Severino FP, Bindu DS, Savage JT, Eroglu C. Astrocyte-secreted neurocan controls inhibitory synapse formation and function. Neuron 2024; 112:1657-1675.e10. [PMID: 38574730 PMCID: PMC11098688 DOI: 10.1016/j.neuron.2024.03.007] [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: 04/18/2023] [Revised: 01/22/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
Astrocytes strongly promote the formation and maturation of synapses by secreted proteins. Several astrocyte-secreted synaptogenic proteins controlling excitatory synapse development were identified; however, those that induce inhibitory synaptogenesis remain elusive. Here, we identify neurocan as an astrocyte-secreted inhibitory synaptogenic protein. After secretion from astrocytes, neurocan is cleaved into N- and C-terminal fragments. We found that these fragments have distinct localizations in the extracellular matrix. The neurocan C-terminal fragment localizes to synapses and controls cortical inhibitory synapse formation and function. Neurocan knockout mice lacking the whole protein or only its C-terminal synaptogenic domain have reduced inhibitory synapse numbers and function. Through super-resolution microscopy, in vivo proximity labeling by secreted TurboID, and astrocyte-specific rescue approaches, we discovered that the synaptogenic domain of neurocan localizes to somatostatin-positive inhibitory synapses and strongly regulates their formation. Together, our results unveil a mechanism through which astrocytes control circuit-specific inhibitory synapse development in the mammalian brain.
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Affiliation(s)
- Dolores Irala
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Shiyi Wang
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kristina Sakers
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Leykashree Nagendren
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Francesco Paolo Ulloa Severino
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Psychology and Neuroscience, Duke University, Durham, NC 27710, USA; Instituto Cajal, CSIC 28002 Madrid, Spain
| | | | - Justin T Savage
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cagla Eroglu
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Psychology and Neuroscience, Duke University, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences (DIBS), Durham, NC 27710, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27710, USA.
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34
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Shin S, Lee SY, Kang MG, Jang DG, Kim J, Rhee HW, Kim JS. Super-resolution proximity labeling with enhanced direct identification of biotinylation sites. Commun Biol 2024; 7:554. [PMID: 38724559 PMCID: PMC11082246 DOI: 10.1038/s42003-024-06112-w] [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: 08/24/2023] [Accepted: 03/26/2024] [Indexed: 05/12/2024] Open
Abstract
Promiscuous labeling enzymes, such as APEX2 or TurboID, are commonly used in in situ biotinylation studies of subcellular proteomes or protein-protein interactions. Although the conventional approach of enriching biotinylated proteins is widely implemented, in-depth identification of specific biotinylation sites remains challenging, and current approaches are technically demanding with low yields. A novel method to systematically identify specific biotinylation sites for LC-MS analysis followed by proximity labeling showed excellent performance compared with that of related approaches in terms of identification depth with high enrichment power. The systematic identification of biotinylation sites enabled a simpler and more efficient experimental design to identify subcellular localized proteins within membranous organelles. Applying this method to the processing body (PB), a non-membranous organelle, successfully allowed unbiased identification of PB core proteins, including novel candidates. We anticipate that our newly developed method will replace the conventional method for identifying biotinylated proteins labeled by promiscuous labeling enzymes.
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Affiliation(s)
- Sanghee Shin
- Center for RNA Research, Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
- The Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Dong-Gi Jang
- Center for RNA Research, Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hyun-Woo Rhee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
| | - Jong-Seo Kim
- Center for RNA Research, Institute of Basic Science, Seoul National University, Seoul, 08826, Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
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35
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Mischley V, Maier J, Chen J, Karanicolas J. PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.16.585347. [PMID: 38559274 PMCID: PMC10979958 DOI: 10.1101/2024.03.16.585347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein-protein interactions underlie nearly all cellular processes. With the advent of protein structure prediction methods such as AlphaFold2 (AF2), models of specific protein pairs can be built extremely accurately in most cases. However, determining the relevance of a given protein pair remains an open question. It is presently unclear how to use best structure-based tools to infer whether a pair of candidate proteins indeed interact with one another: ideally, one might even use such information to screen amongst candidate pairings to build up protein interaction networks. Whereas methods for evaluating quality of modeled protein complexes have been co-opted for determining which pairings interact (e.g., pDockQ and iPTM), there have been no rigorously benchmarked methods for this task. Here we introduce PPIscreenML, a classification model trained to distinguish AF2 models of interacting protein pairs from AF2 models of compelling decoy pairings. We find that PPIscreenML out-performs methods such as pDockQ and iPTM for this task, and further that PPIscreenML exhibits impressive performance when identifying which ligand/receptor pairings engage one another across the structurally conserved tumor necrosis factor superfamily (TNFSF). Analysis of benchmark results using complexes not seen in PPIscreenML development strongly suggest that the model generalizes beyond training data, making it broadly applicable for identifying new protein complexes based on structural models built with AF2.
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Affiliation(s)
- Victoria Mischley
- Cancer Signaling & Microenvironment Program, Fox Chase Cancer Center, Philadelphia PA 19111
- Molecular Cell Biology and Genetics, Drexel University, Philadelphia PA 19102
| | | | | | - John Karanicolas
- Cancer Signaling & Microenvironment Program, Fox Chase Cancer Center, Philadelphia PA 19111
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia PA 19140
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36
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Lu Z, Xie S, Su H, Han S, Huang H, Zhou X. Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase. Nucleic Acids Res 2024; 52:e37. [PMID: 38452210 PMCID: PMC11040147 DOI: 10.1093/nar/gkae126] [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: 09/19/2023] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 03/09/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures pivotal to cellular processes and disease pathways. Deciphering G4-interacting proteins is imperative for unraveling G4's biological significance. In this study, we developed a G4-targeting biotin ligase named G4PID, meticulously assessing its binding affinity and specificity both in vitro and in vivo. Capitalizing on G4PID, we devised a tailored approach termed G-quadruplex-interacting proteins specific biotin-ligation procedure (PLGPB) to precisely profile G4-interacting proteins. Implementing this innovative strategy in live cells, we unveiled a cohort of 149 potential G4-interacting proteins, which exhibiting multifaceted functionalities. We then substantiate the directly binding affinity of 7 candidate G4-interacting-proteins (SF3B4, FBL, PP1G, BCL7C, NDUV1, ILF3, GAR1) in vitro. Remarkably, we verified that splicing factor 3B subunit 4 (SF3B4) binds preferentially to the G4-rich 3' splice site and the corresponding splicing sites are modulated by the G4 stabilizer PDS, indicating the regulating role of G4s in mRNA splicing procedure. The PLGPB strategy could biotinylate multiple proteins simultaneously, which providing an opportunity to map G4-interacting proteins network in living cells.
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Affiliation(s)
- Ziang Lu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Shengjie Xie
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Haomiao Su
- Department of Chemistry, Yale University, 600 West Campus Drive West Haven, West Haven, CT 06516, USA
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Haiyan Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
- Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, P.R. China
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37
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Reina J, Vallmajo-Martin Q, Ning J, Michi AN, Yeung K, Wahl GM, Hunter T. LHPP expression in triple-negative breast cancer promotes tumor growth and metastasis by modulating the tumor microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590151. [PMID: 38712081 PMCID: PMC11071390 DOI: 10.1101/2024.04.19.590151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive and metastatic form of breast cancer that lacks an effective targeted therapy. To identify new therapeutic targets, we investigated the phosphohistidine phosphatase, LHPP, which has been implicated in the development of several types of cancer. However, the full significance of LHPP in cancer progression remains unclear due to our limited understanding of its molecular mechanism. We found that levels of the LHPP phosphohistidine phosphatase were significantly increased in human breast cancer patients compared to normal adjacent tissues, with the highest levels in the TNBC subtype. When LHPP was knocked out in the MDA-MB-231 human TNBC cell line, cell proliferation, wound healing capacity, and invasion were significantly reduced. However, LHPP knockout in TNBC cells did not affect the phosphohistidine protein levels. Interestingly, LHPP knockout in MDA-MB-231 cells delayed tumor growth and reduced metastasis when orthotopically transplanted into mouse mammary glands. To investigate LHPP's role in breast cancer progression, we used next-generation sequencing and proximity-labeling proteomics, and found that LHPP regulates gene expression in chemokine-mediated signaling and actin cytoskeleton organization. Depletion of LHPP reduced the presence of tumor-infiltrating macrophages in mouse xenografts. Our results uncover a new tumor promoter role for LHPP phosphohistidine phosphatase in TNBC and suggest that targeting LHPP phosphatase could be a potential therapeutic strategy for TNBC.
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Affiliation(s)
- Jeffrey Reina
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Jia Ning
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Aubrey N Michi
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kay Yeung
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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38
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Cui C, Hao P, Jin C, Xu W, Liu Y, Li L, Du S, Shang L, Jin X, Jin N, Wang J, Li C. Interaction of Nipah Virus F and G with the Cellular Protein Cortactin Discovered by a Proximity Interactome Assay. Int J Mol Sci 2024; 25:4112. [PMID: 38612921 PMCID: PMC11012870 DOI: 10.3390/ijms25074112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Nipah virus (NiV) is a highly lethal zoonotic virus with a potential large-scale outbreak, which poses a great threat to world health and security. In order to explore more potential factors associated with NiV, a proximity labeling method was applied to investigate the F, G, and host protein interactions systematically. We screened 1996 and 1524 high-confidence host proteins that interacted with the NiV fusion (F) glycoprotein and attachment (G) glycoprotein in HEK293T cells by proximity labeling technology, and 863 of them interacted with both F and G. The results of GO and KEGG enrichment analysis showed that most of these host proteins were involved in cellular processes, molecular binding, endocytosis, tight junction, and other functions. Cytoscape software (v3.9.1) was used for visual analysis, and the results showed that Cortactin (CTTN), Serpine mRNA binding protein 1 (SERBP1), and stathmin 1 (STMN1) were the top 20 proteins and interacted with F and G, and were selected for further validation. We observed colocalization of F-CTTN, F-SERBP1, F-STMN1, G-CTTN, G-SERBP1, and G-STMN1 using confocal fluorescence microscopy, and the results showed that CTTN, SERBP1, and STMN1 overlapped with NiV F and NiV G in HEK293T cells. Further studies found that CTTN can significantly inhibit the infection of the Nipah pseudovirus (NiVpv) into host cells, while SERBP1 and STMN1 had no significant effect on pseudovirus infection. In addition, CTTN can also inhibit the infection of the Hendra pseudovirus (HeVpv) in 293T cells. In summary, this study revealed that the potential host proteins interacted with NiV F and G and demonstrated that CTTN could inhibit NiVpv and HeVpv infection, providing new evidence and targets for the study of drugs against these diseases.
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Affiliation(s)
- Chunmei Cui
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
- Preventive Veterinary Medicine Laboratory of Agricultural College, Yanbian University, Yanji 133000, China;
| | - Pengfei Hao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Chaozhi Jin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (C.J.); (Y.L.); (L.S.)
| | - Wang Xu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Yuchen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (C.J.); (Y.L.); (L.S.)
| | - Letian Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Shouwen Du
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Limin Shang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (C.J.); (Y.L.); (L.S.)
| | - Xin Jin
- Preventive Veterinary Medicine Laboratory of Agricultural College, Yanbian University, Yanji 133000, China;
| | - Ningyi Jin
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (C.J.); (Y.L.); (L.S.)
| | - Chang Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.C.); (P.H.); (W.X.); (L.L.); (S.D.); (N.J.)
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Sarihan M, Kasap M, Akpinar G. Streamlined Biotinylation, Enrichment and Analysis for Enhanced Plasma Membrane Protein Identification Using TurboID and TurboID-Start Biotin Ligases. J Membr Biol 2024; 257:91-105. [PMID: 38289568 DOI: 10.1007/s00232-023-00303-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/23/2023] [Indexed: 04/11/2024]
Abstract
Plasma membrane proteins (PMPs) play pivotal roles in various cellular events and are crucial in disease pathogenesis, making their comprehensive characterization vital for biomedical research. However, the hydrophobic nature and low expression levels of PMPs pose challenges for conventional enrichment methods, hindering their identification and functional profiling. In this study, we presented a novel TurboID-based enrichment approach for PMPs that helped overcoming some of the existing limitations. We evaluated the efficacy of TurboID and its modified form, TurboID-START, in PMP enrichment, achieving efficient and targeted labelling of PMPs without the need for stable cell line generation. This approach resulted reduction in non-specific biotinylation events, leading to improved PMP enrichment and enabled assessment of the subcellular proteome associated with the plasma membrane. Our findings paved the way for studies targeting the dynamic nature of the plasma membrane proteome and aiming to capture transient associations of proteins with the plasma membrane. The novel TurboID-based enrichment approach presented here offers promising prospects for in-depth investigations into PMPs and their roles in cellular processes.
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Affiliation(s)
- Mehmet Sarihan
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey.
| | - Gurler Akpinar
- Department of Medical Biology/Proteomics Laboratory, Kocaeli University Medical School, 41001, Umuttepe, Kocaeli, Turkey
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40
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Liu J, Isaji T, Komatsu S, Sun Y, Xu X, Fukuda T, Fujimura T, Takahashi S, Gu J. BRCC36 associates with FLT3-ITD to regulate its protein stability and intracellular signaling in acute myeloid leukemia. Cancer Sci 2024; 115:1196-1208. [PMID: 38288901 PMCID: PMC11007003 DOI: 10.1111/cas.16090] [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: 07/21/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 04/12/2024] Open
Abstract
Fms-like tyrosine kinase-3 (FLT3) is a commonly mutated gene in acute myeloid leukemia (AML). The two most common mutations are the internal-tandem duplication domain (ITD) mutation and the tyrosine kinase domain (TKD) mutation. FLT3-ITD and FLT3-TKD exhibit distinct protein stability, cellular localization, and intracellular signaling. To understand the underlying mechanisms, we performed proximity labeling with TurboID to identify proteins that regulate FLT3-ITD or -TKD differently. We found that BRCA1/BRCA2-containing complex subunit 36 (BRCC36), a specific K63-linked polyubiquitin deubiquitinase, was exclusively associated with ITD, not the wild type of FLT3 and TKD. Knockdown of BRCC36 resulted in decreased signal transducers and activators of transcription 5 phosphorylation and cell proliferation in ITD cells. Consistently, treatment with thiolutin, an inhibitor of BRCC36, specifically suppressed cell proliferation and induced cell apoptosis in ITD cells. Thiolutin efficiently affected leukemia cell lines expressing FLT3-ITD cell viability and exhibited mutual synergies with quizartinib, a standard clinical medicine for AML. Furthermore, mutation of the lysine at 609 of ITD led to significant suppression of K63 polyubiquitination and decreased its stability, suggesting that K609 is a critical site for K63 ubiquitination specifically recognized by BRCC36. These data indicate that BRCC36 is a specific regulator for FLT3-ITD, which may shed light on developing a novel therapeutic approach for AML.
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Affiliation(s)
- Jianwei Liu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Tomoya Isaji
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Sachiko Komatsu
- Division of Bioanalytical ChemistryTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Yuhan Sun
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Xing Xu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Tomohiko Fukuda
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Tsutomu Fujimura
- Division of Bioanalytical ChemistryTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Shinichiro Takahashi
- Division of Laboratory Medicine, Faculty of MedicineTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
| | - Jianguo Gu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and GlycobiologyTohoku Medical and Pharmaceutical UniversitySendaiMiyagiJapan
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41
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Fu Y, Zhou Y, Wang K, Li Z, Kong W. Extracellular Matrix Interactome in Modulating Vascular Homeostasis and Remodeling. Circ Res 2024; 134:931-949. [PMID: 38547250 DOI: 10.1161/circresaha.123.324055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The ECM (extracellular matrix) is a major component of the vascular microenvironment that modulates vascular homeostasis. ECM proteins include collagens, elastin, noncollagen glycoproteins, and proteoglycans/glycosaminoglycans. ECM proteins form complex matrix structures, such as the basal lamina and collagen and elastin fibers, through direct interactions or lysyl oxidase-mediated cross-linking. Moreover, ECM proteins directly interact with cell surface receptors or extracellular secreted molecules, exerting matricellular and matricrine modulation, respectively. In addition, extracellular proteases degrade or cleave matrix proteins, thereby contributing to ECM turnover. These interactions constitute the ECM interactome network, which is essential for maintaining vascular homeostasis and preventing pathological vascular remodeling. The current review mainly focuses on endogenous matrix proteins in blood vessels and discusses the interaction of these matrix proteins with other ECM proteins, cell surface receptors, cytokines, complement and coagulation factors, and their potential roles in maintaining vascular homeostasis and preventing pathological remodeling.
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Affiliation(s)
- Yi Fu
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yuan Zhou
- Department of Biomedical Informatics (Y.Z.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Kai Wang
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Zhuofan Li
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Wei Kong
- Department of Physiology and Pathophysiology (Y.F., K.W., Z.L., W.K.), School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
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42
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Shi Y, Bashian EE, Hou Y, Wu P. Chemical immunology: Recent advances in tool development and applications. Cell Chem Biol 2024; 31:S2451-9456(24)00080-1. [PMID: 38508196 PMCID: PMC11393185 DOI: 10.1016/j.chembiol.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Immunology was one of the first biological fields to embrace chemical approaches. The development of new chemical approaches and techniques has provided immunologists with an impressive arsenal of tools to address challenges once considered insurmountable. This review focuses on advances at the interface of chemistry and immunobiology over the past two decades that have not only opened new avenues in basic immunological research, but also revolutionized drug development for the treatment of cancer and autoimmune diseases. These include chemical approaches to understand and manipulate antigen presentation and the T cell priming process, to facilitate immune cell trafficking and regulate immune cell functions, and therapeutic applications of chemical approaches to disease control and treatment.
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Affiliation(s)
- Yujie Shi
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eleanor E Bashian
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yingqin Hou
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peng Wu
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Lim B, Domsch K, Mall M, Lohmann I. Canalizing cell fate by transcriptional repression. Mol Syst Biol 2024; 20:144-161. [PMID: 38302581 PMCID: PMC10912439 DOI: 10.1038/s44320-024-00014-z] [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: 09/19/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024] Open
Abstract
Precision in the establishment and maintenance of cellular identities is crucial for the development of multicellular organisms and requires tight regulation of gene expression. While extensive research has focused on understanding cell type-specific gene activation, the complex mechanisms underlying the transcriptional repression of alternative fates are not fully understood. Here, we provide an overview of the repressive mechanisms involved in cell fate regulation. We discuss the molecular machinery responsible for suppressing alternative fates and highlight the crucial role of sequence-specific transcription factors (TFs) in this process. Depletion of these TFs can result in unwanted gene expression and increased cellular plasticity. We suggest that these TFs recruit cell type-specific repressive complexes to their cis-regulatory elements, enabling them to modulate chromatin accessibility in a context-dependent manner. This modulation effectively suppresses master regulators of alternative fate programs and their downstream targets. The modularity and dynamic behavior of these repressive complexes enables a limited number of repressors to canalize and maintain major and minor cell fate decisions at different stages of development.
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Affiliation(s)
- Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks - Cluster of Excellence, Heidelberg, Germany.
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44
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Soto JS, Jami-Alahmadi Y, Wohlschlegel JA, Khakh BS. In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation. Nat Protoc 2024; 19:896-927. [PMID: 38062165 DOI: 10.1038/s41596-023-00923-7] [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: 08/03/2023] [Accepted: 10/03/2023] [Indexed: 02/08/2024]
Abstract
The central nervous system (CNS) comprises diverse and morphologically complex cells. To understand the molecular basis of their physiology, it is crucial to assess proteins expressed within intact cells. Commonly used methods utilize cell dissociation and sorting to isolate specific cell types such as neurons and astrocytes, the major CNS cells. Proteins purified from isolated cells are identified by mass spectrometry-based proteomics. However, dissociation and cell-sorting methods lead to near total loss of cellular morphology, thereby losing proteins from key relevant subcompartments such as processes, end feet, dendrites and axons. Here we provide a systematic protocol for cell- and subcompartment-specific labeling and identification of proteins found within intact astrocytes and neurons in vivo. This protocol utilizes the proximity-dependent biotinylation system BioID2, selectively expressed in either astrocytes or neurons, to label proximal proteins in a cell-specific manner. BioID2 is targeted genetically to assess the subproteomes of subcellular compartments such as the plasma membrane and sites of cell-cell contacts. We describe in detail the expression methods (variable timing), stereotaxic surgeries for expression (1-2 d and then 3 weeks), in vivo protein labeling (7 d), protein isolation (2-3 d), protein identification methods (2-3 d) and data analysis (1 week). The protocol can be applied to any area of the CNS in mouse models of physiological processes and for disease-related research.
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Affiliation(s)
- Joselyn S Soto
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Baljit S Khakh
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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45
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Ray S, DeSilva C, Dasgupta I, Mana-Capelli S, Cruz-Calderon N, McCollum D. The ability of the LIMD1 and TRIP6 LIM domains to bind strained f-actin is critical for their tension dependent localization to adherens junctions and association with the Hippo pathway kinase LATS1. Cytoskeleton (Hoboken) 2024:10.1002/cm.21847. [PMID: 38426816 PMCID: PMC11366040 DOI: 10.1002/cm.21847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
A key step in regulation of Hippo pathway signaling in response to mechanical tension is recruitment of the LIM domain proteins TRIP6 and LIMD1 to adherens junctions. Mechanical tension also triggers TRIP6 and LIMD1 to bind and inhibit the Hippo pathway kinase LATS1. How TRIP6 and LIMD1 are recruited to adherens junctions in response to tension is not clear, but previous studies suggested that they could be regulated by the known mechanosensory proteins α-catenin and vinculin at adherens junctions. We found that the three LIM domains of TRIP6 and LIMD1 are necessary and sufficient for tension-dependent localization to adherens junctions. The LIM domains of TRIP6, LIMD1, and certain other LIM domain proteins have been shown to bind to actin networks under strain/tension. Consistent with this, we show that TRIP6 and LIMD1 colocalize with the ends of actin fibers at adherens junctions. Point mutations in a key conserved residue in each LIM domain that are predicted to impair binding to f-actin under strain inhibits TRIP6 and LIMD1 localization to adherens junctions and their ability to bind to and recruit LATS1 to adherens junctions. Together these results show that the ability of TRIP6 and LIMD1 to bind to strained actin underlies their ability to localize to adherens junctions and regulate LATS1 in response to mechanical tension.
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Affiliation(s)
- Samriddha Ray
- Department of Biochemistry & Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, 01605
| | - Chamika DeSilva
- Department of Biochemistry & Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, 01605
| | - Ishani Dasgupta
- Department of Biochemistry & Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, 01605
| | - Sebastian Mana-Capelli
- Department of Biochemistry & Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, 01605
| | - Natasha Cruz-Calderon
- Department of Biochemistry & Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, 01605
| | - Dannel McCollum
- Department of Biochemistry & Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, 01605
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46
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Martinez D, Jiang E, Zhou Z. Overcoming genetic and cellular complexity to study the pathophysiology of X-linked intellectual disabilities. J Neurodev Disord 2024; 16:5. [PMID: 38424476 PMCID: PMC10902969 DOI: 10.1186/s11689-024-09517-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
X-linked genetic causes of intellectual disability (ID) account for a substantial proportion of cases and remain poorly understood, in part due to the heterogeneous expression of X-linked genes in females. This is because most genes on the X chromosome are subject to random X chromosome inactivation (XCI) during early embryonic development, which results in a mosaic pattern of gene expression for a given X-linked mutant allele. This mosaic expression produces substantial complexity, especially when attempting to study the already complicated neural circuits that underly behavior, thus impeding the understanding of disease-related pathophysiology and the development of therapeutics. Here, we review a few selected X-linked forms of ID that predominantly affect heterozygous females and the current obstacles for developing effective therapies for such disorders. We also propose a genetic strategy to overcome the complexity presented by mosaicism in heterozygous females and highlight specific tools for studying synaptic and circuit mechanisms, many of which could be shared across multiple forms of intellectual disability.
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Affiliation(s)
- Dayne Martinez
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Evan Jiang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA
| | - Zhaolan Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Medical Scientist Training Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19102, USA.
- Intellectual and Developmental Disabilities Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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47
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Islam S, Gour J, Beer T, Tang HY, Cassel J, Salvino JM, Busino L. A Tandem-Affinity Purification Method for Identification of Primary Intracellular Drug-Binding Proteins. ACS Chem Biol 2024; 19:233-242. [PMID: 38271588 PMCID: PMC10878392 DOI: 10.1021/acschembio.3c00570] [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: 09/14/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
In the field of drug discovery, understanding how small molecule drugs interact with cellular components is crucial. Our study introduces a novel methodology to uncover primary drug targets using Tandem Affinity Purification for identification of Drug-Binding Proteins (TAP-DBP). Central to our approach is the generation of a FLAG-hemagglutinin (HA)-tagged chimeric protein featuring the FKBP12(F36V) adaptor protein and the TurboID enzyme. Conjugation of drug molecules with the FKBP12(F36V) ligand allows for the coordinated recruitment of drug-binding partners effectively enabling in-cell TurboID-mediated biotinylation. By employing a tandem affinity purification protocol based on FLAG-immunoprecipitation and streptavidin pulldown, alongside mass spectrometry analysis, TAP-DBP allows for the precise identification of drug-primary binding partners. Overall, this study introduces a systematic, unbiased method for identification of drug-protein interactions, contributing a clear understanding of target engagement and drug selectivity to advance the mode of action of a drug in cells.
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Affiliation(s)
- Sehbanul Islam
- University
of Pennsylvania, Perelman School
of Medicine, Department of Cancer Biology, Philadelphia, Pennsylvania 19104, United States
| | - Jitendra Gour
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Thomas Beer
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Hsin-Yao Tang
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Joel Cassel
- Molecular
Screening and Protein Expression Shared Resource, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Joseph M. Salvino
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Luca Busino
- University
of Pennsylvania, Perelman School
of Medicine, Department of Cancer Biology, Philadelphia, Pennsylvania 19104, United States
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48
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Caudal A, Snyder MP, Wu JC. Harnessing human genetics and stem cells for precision cardiovascular medicine. CELL GENOMICS 2024; 4:100445. [PMID: 38359791 PMCID: PMC10879032 DOI: 10.1016/j.xgen.2023.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/22/2023] [Accepted: 10/25/2023] [Indexed: 02/17/2024]
Abstract
Human induced pluripotent stem cell (iPSC) platforms are valuable for biomedical and pharmaceutical research by providing tissue-specific human cells that retain patients' genetic integrity and display disease phenotypes in a dish. Looking forward, combining iPSC phenotyping platforms with genomic and screening technologies will continue to pave new directions for precision medicine, including genetic prediction, visualization, and treatment of heart disease. This review summarizes the recent use of iPSC technology to unpack the influence of genetic variants in cardiovascular pathology. We focus on various state-of-the-art genomic tools for cardiovascular therapies-including the expansion of genetic toolkits for molecular interrogation, in vitro population studies, and function-based drug screening-and their current applications in patient- and genome-edited iPSC platforms that are heralding new avenues for cardiovascular research.
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Affiliation(s)
- Arianne Caudal
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Greenstone Biosciences, Palo Alto, CA 94304, USA.
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Fordyce BA, Roth BL. Making Sense of Psychedelics in the CNS. Int J Neuropsychopharmacol 2024; 27:pyae007. [PMID: 38289825 PMCID: PMC10888522 DOI: 10.1093/ijnp/pyae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/29/2024] [Indexed: 02/01/2024] Open
Abstract
For centuries, ancient lineages have consumed psychedelic compounds from natural sources. In the modern era, scientists have since harnessed the power of computational tools, cellular assays, and behavioral metrics to study how these compounds instigate changes on molecular, cellular, circuit-wide, and system levels. Here, we provide a brief history of psychedelics and their use in science, medicine, and culture. We then outline current techniques for studying psychedelics from a pharmacological perspective. Finally, we address known gaps in the field and potential avenues of further research to broaden our collective understanding of physiological changes induced by psychedelics, the limits of their therapeutic capabilities, and how researchers can improve and inform treatments that are rapidly becoming accessible worldwide.
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Affiliation(s)
- Blake A Fordyce
- Department of Neuroscience, UNC Chapel Hill Medical School Chapel Hill, North Carolina, USA
| | - Bryan L Roth
- Department of Pharmacology, UNC Chapel Hill Medical School Chapel Hill, North Carolina, USA
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Paul B, Merta H, Ugrankar-Banerjee R, Hensley M, Tran S, Dias do Vale G, McDonald JG, Farber SA, Henne WM. Paraoxonase-like APMAP maintains endoplasmic reticulum-associated lipid and lipoprotein homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577049. [PMID: 38328083 PMCID: PMC10849633 DOI: 10.1101/2024.01.26.577049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Oxidative stress perturbs lipid homeostasis and contributes to metabolic diseases. Though ignored compared to mitochondrial oxidation, the endoplasmic reticulum (ER) generates reactive oxygen species requiring antioxidant quality control. Using multi-organismal profiling featuring Drosophila, zebrafish, and mammalian cells, here we characterize the paraoxonase-like APMAP as an ER-localized protein that promotes redox and lipid homeostasis and lipoprotein maturation. APMAP-depleted mammalian cells exhibit defective ER morphology, elevated ER and oxidative stress, lipid droplet accumulation, and perturbed ApoB-lipoprotein homeostasis. Critically, APMAP loss is rescued with chemical antioxidant NAC. Organismal APMAP depletion in Drosophila perturbs fat and lipoprotein homeostasis, and zebrafish display increased vascular ApoB-containing lipoproteins, particles that are atherogenic in mammals. Lipidomics reveals altered polyunsaturated phospholipids and increased ceramides upon APMAP loss, which perturbs ApoB-lipoprotein maturation. These ApoB-associated defects are rescued by inhibiting ceramide synthesis. Collectively, we propose APMAP is an ER-localized antioxidant that promotes lipid and lipoprotein homeostasis.
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Affiliation(s)
- Blessy Paul
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Holly Merta
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390
| | | | - Monica Hensley
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Son Tran
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Goncalo Dias do Vale
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Jeffrey G McDonald
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Steven A Farber
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390
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