1
|
Sun S, Li C, Hou H, Li J. Protein-metabolite Interactions Based on Chemical Targeting Methods. Chembiochem 2025; 26:e202400852. [PMID: 39715006 DOI: 10.1002/cbic.202400852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 12/02/2024] [Accepted: 12/18/2024] [Indexed: 12/25/2024]
Abstract
The importance of the protein-metabolite interaction network extends beyond its relevance to life sciences focused on proteins, it also profoundly influences its mechanisms related to disease targets, drug screening, and clinical diagnosis and treatment. Research methods targeting protein-metabolite interaction focus on enhancing the detectable signals of specific interactions by examining the structural characteristics of both proteins and metabolites in conjunction with chemical molecules, playing a crucial role in elucidating the protein-metabolite interaction network. Consequently, this article outlines several chemical targeting strategies developed in recent years and provides examples of their applications in the discovery and interpretation of new protein-metabolite interaction pathways. Finally, a brief summary will be presented regarding technological advances, research prospects, and current challenges of protein-metabolite interaction research.
Collapse
Affiliation(s)
- Shuzhe Sun
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Chuntong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Hongwei Hou
- Beijing Life Science Academy, Beijing, 102209, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Beijing Life Science Academy, Beijing, 102209, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| |
Collapse
|
2
|
Chen PHB, Li XL, Baskin JM. Synthetic Lipid Biology. Chem Rev 2025; 125:2502-2560. [PMID: 39805091 PMCID: PMC11969270 DOI: 10.1021/acs.chemrev.4c00761] [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] [Indexed: 01/16/2025]
Abstract
Cells contain thousands of different lipids. Their rapid and redundant metabolism, dynamic movement, and many interactions with other biomolecules have justly earned lipids a reputation as a vexing class of molecules to understand. Further, as the cell's hydrophobic metabolites, lipids assemble into supramolecular structures─most commonly bilayers, or membranes─from which they carry out myriad biological functions. Motivated by this daunting complexity, researchers across disciplines are bringing order to the seeming chaos of biological lipids and membranes. Here, we formalize these efforts as "synthetic lipid biology". Inspired by the idea, central to synthetic biology, that our abilities to understand and build biological systems are intimately connected, we organize studies and approaches across numerous fields to create, manipulate, and analyze lipids and biomembranes. These include construction of lipids and membranes from scratch using chemical and chemoenzymatic synthesis, editing of pre-existing membranes using optogenetics and protein engineering, detection of lipid metabolism and transport using bioorthogonal chemistry, and probing of lipid-protein interactions and membrane biophysical properties. What emerges is a portrait of an incipient field where chemists, biologists, physicists, and engineers work together in proximity─like lipids themselves─to build a clearer description of the properties, behaviors, and functions of lipids and membranes.
Collapse
Affiliation(s)
- Po-Hsun Brian Chen
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xiang-Ling Li
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
3
|
Cai H, Zhang H, Xin G, Peng S, Xu F, Zhang N, Li Y, Zhang W, Li Y, Ren Y, Wang Y, Liu Z, Kong X, Wang L. Identification of Key Genes and Immune Characteristics of SASP in Acute Ischemic Stroke. J Mol Neurosci 2025; 75:22. [PMID: 39960563 DOI: 10.1007/s12031-025-02312-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: 11/25/2024] [Accepted: 01/18/2025] [Indexed: 04/02/2025]
Abstract
The senescence-associated secretory phenotype (SASP) is a key mechanism through which senescent cardiovascular cells contribute to plaque formation, instability, and vascular remodeling. However, the correlation between SASP and acute ischemic stroke (AIS), particularly its immune inflammation characteristics, remains underexplored and requires further elucidation. We downloaded the AIS database from the GEO database and obtained SASP genes from the SASP Atlas and related literature. Using two machine learning algorithms, we identified five hub genes. Unsupervised cluster analysis was performed on patients with AIS and DEGs separately to identify distinct gene clusters, which were then analyzed for immune characteristics. We then explored the related biological functions and immune properties of the hub genes by using various algorithms (GSEA, GSVA, and CIBERSORT). Principal component analysis (PCA) was used to generate SASP-related gene scores based on the expression of hub genes. A logistic regression algorithm was employed to establish an AIS classification diagnosis model based on the hub genes. Peripheral venous blood was collected for validation using real-time quantitative PCR (RT-qPCR). We identified five hub genes using two machine learning algorithms and validated them with RT-qPCR. Gene cluster analysis revealed two distinct clusters, SASP-related gene cluster B and differentially expressed gene cluster B, indicating that the acute AIS samples had more severe immune inflammatory response and a higher risk of disease deterioration. We constructed a gene-drug regulatory network for PIN1 and established an AIS diagnostic model and nomogram using a logistic regression algorithm. This study explored the gene expression, molecular patterns, and immunological characteristics of SASP in patients with AIS using bioinformatic methods. It provides a theoretical basis and research direction for identifying new diagnostic markers for AIS, understanding the molecular mechanism of thrombosis, and improving the classification, diagnosis, treatment, and prognosis of AIS.
Collapse
Affiliation(s)
- Hanlu Cai
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Huixue Zhang
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Guanghao Xin
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Shanshan Peng
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Fanfan Xu
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Nan Zhang
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Yichen Li
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Wei Zhang
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Ying Li
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Yingjie Ren
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Yu Wang
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Zhaojun Liu
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Xiaotong Kong
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China.
| | - Lihua Wang
- The Second Affiliated Hospital, Harbin Medical University, Heilongjiang Province, Harbin, 150086, China.
| |
Collapse
|
4
|
Perry AS, Amancherla K, Huang X, Lance ML, Farber-Eger E, Gajjar P, Amrute J, Stolze L, Zhao S, Sheng Q, Joynes CM, Peng Z, Tanaka T, Drakos SG, Lavine KJ, Selzman C, Visker JR, Shankar TS, Ferrucci L, Das S, Wilcox J, Patel RB, Kalhan R, Shah SJ, Walker KA, Wells Q, Tucker N, Nayor M, Shah RV, Khan SS. Clinical-transcriptional prioritization of the circulating proteome in human heart failure. Cell Rep Med 2024; 5:101704. [PMID: 39226894 PMCID: PMC11524958 DOI: 10.1016/j.xcrm.2024.101704] [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: 12/15/2023] [Revised: 06/15/2024] [Accepted: 08/07/2024] [Indexed: 09/05/2024]
Abstract
Given expanding studies in epidemiology and disease-oriented human studies offering hundreds of associations between the human "ome" and disease, prioritizing molecules relevant to disease mechanisms among this growing breadth is important. Here, we link the circulating proteome to human heart failure (HF) propensity (via echocardiographic phenotyping and clinical outcomes) across the lifespan, demonstrating key pathways of fibrosis, inflammation, metabolism, and hypertrophy. We observe a broad array of genes encoding proteins linked to HF phenotypes and outcomes in clinical populations dynamically expressed at a transcriptional level in human myocardium during HF and cardiac recovery (several in a cell-specific fashion). Many identified targets do not have wide precedent in large-scale genomic discovery or human studies, highlighting the complementary roles for proteomic and tissue transcriptomic discovery to focus epidemiological targets to those relevant in human myocardium for further interrogation.
Collapse
Affiliation(s)
- Andrew S Perry
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kaushik Amancherla
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xiaoning Huang
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Eric Farber-Eger
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Priya Gajjar
- Sections of Cardiovascular Medicine and Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Junedh Amrute
- Cardiology Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsey Stolze
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cassandra M Joynes
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Zhongsheng Peng
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Stavros G Drakos
- Division of Cardiovascular Medicine, University of Utah and Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), Salt Lake City, UT, USA
| | - Kory J Lavine
- Cardiology Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Craig Selzman
- Department of Cardiac Surgery, University of Utah School of Medicine, Division of Cardiothoracic Surgery, University of Utah and Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), Salt Lake City, UT, USA
| | - Joseph R Visker
- Division of Cardiovascular Medicine, University of Utah and Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), Salt Lake City, UT, USA
| | - Thirupura S Shankar
- Division of Cardiovascular Medicine, University of Utah and Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), Salt Lake City, UT, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Saumya Das
- Cardiovascular Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jane Wilcox
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ravi B Patel
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ravi Kalhan
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sanjiv J Shah
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Keenan A Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Quinn Wells
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Matthew Nayor
- Sections of Cardiovascular Medicine and Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ravi V Shah
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Sadiya S Khan
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| |
Collapse
|
5
|
Li T, Wang A, Zhang Y, Chen W, Guo Y, Yuan X, Liu Y, Geng Y. Chemoproteomic Profiling of Signaling Metabolite Fructose-1,6-Bisphosphate Interacting Proteins in Living Cells. J Am Chem Soc 2024; 146:15155-15166. [PMID: 38775806 DOI: 10.1021/jacs.4c01335] [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: 06/06/2024]
Abstract
Fructose-1,6-bisphosphate (FBP), a cellular endogenous sugar metabolite in the glycolytic pathway, has recently been reported to act as a signaling molecule to regulate various cellular events through the engagement of important proteins. Though tremendous progress has been made in identifying specific FBP-protein interactions, the comprehensive identification of FBP-interacting proteins and their regulatory mechanisms remains largely unexplored. Here, we describe a concise synthetic approach for the scalable preparation of a photoaffinity FBP probe that enables the quantitative chemoproteomic profiling of FBP-protein interactions based on photoaffinity labeling (PAL) directly in living cells. Using such a protocol, we captured known FBP targets including PKM2 and MDH2. Furthermore, among unknown FBP-interacting proteins, we identified a mitochondrial metabolic enzyme aldehyde dehydrogenase 2 (ALDH2), against which FBP showed inhibitory activity and resulted in cellular ROS upregulation accompanied by mitochondrial fragmentation. Our findings disclosed a new mode of glucose signaling mediating by the FBP-ALDH2-ROS axis.
Collapse
Affiliation(s)
- Tian Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Anhui Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yanling Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wei Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yanshen Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yiqun Geng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| |
Collapse
|
6
|
Chakraborty A, Kamat SS. Lysophosphatidylserine: A Signaling Lipid with Implications in Human Diseases. Chem Rev 2024; 124:5470-5504. [PMID: 38607675 DOI: 10.1021/acs.chemrev.3c00701] [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: 04/14/2024]
Abstract
Lysophosphatidylserine (lyso-PS) has emerged as yet another important signaling lysophospholipid in mammals, and deregulation in its metabolism has been directly linked to an array of human autoimmune and neurological disorders. It has an indispensable role in several biological processes in humans, and therefore, cellular concentrations of lyso-PS are tightly regulated to ensure optimal signaling and functioning in physiological settings. Given its biological importance, the past two decades have seen an explosion in the available literature toward our understanding of diverse aspects of lyso-PS metabolism and signaling and its association with human diseases. In this Review, we aim to comprehensively summarize different aspects of lyso-PS, such as its structure, biodistribution, chemical synthesis, and SAR studies with some synthetic analogs. From a biochemical perspective, we provide an exhaustive coverage of the diverse biological activities modulated by lyso-PSs, such as its metabolism and the receptors that respond to them in humans. We also briefly discuss the human diseases associated with aberrant lyso-PS metabolism and signaling and posit some future directions that may advance our understanding of lyso-PS-mediated mammalian physiology.
Collapse
Affiliation(s)
- Arnab Chakraborty
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India
| |
Collapse
|
7
|
Su Y, Han Y, Choi HS, Lee GY, Cho HW, Choi H, Choi JH, Jang YS, Seo JW. Lipid mediators obtained from docosahexaenoic acid by soybean lipoxygenase attenuate RANKL-induced osteoclast differentiation and rheumatoid arthritis. Biomed Pharmacother 2024; 171:116153. [PMID: 38232664 DOI: 10.1016/j.biopha.2024.116153] [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: 11/06/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic immune-mediated inflammatory disease characterized by persistent inflammation and joint destruction. A lipid mediator (LM, namely, 17S-monohydroxy docosahexaenoic acid, resolvin D5, and protectin DX in a ratio of 3:47:50) produced by soybean lipoxygenase from DHA, exhibits anti-inflammatory activity. In this study, we determined the effect of LM on collagen antibody-induced arthritis (CAIA) in mice and receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclast formation in RAW264.7 cells. LM effectively downregulated the expression of tartrate-resistant acid phosphatase (TRAP) and cathepsin K, inhibited osteoclast formation, and suppressed the NF-κB signaling pathway in vitro. In vivo, LM at 10 μg/kg/day significantly decreased paw swelling and inhibited progression of arthritis in CAIA mice. Moreover, proinflammatory cytokine (tumor necrosis factor-α, interleukin (IL)-6, IL-1β, IL-17, and interferon-γ) levels in serum were decreased, whereas IL-10 levels were increased following LM treatment. Furthermore, LM alleviated joint inflammation, cartilage erosion, and bone destruction in the ankles, which may be related to matrix metalloproteinase and Janus kinase (JAK)-signal transducer and activators of transcription (STAT) signaling pathway. Our findings suggest that LM attenuates arthritis severity, restores serum imbalances, and modifies joint damage. Thus, LM represents a promising therapy for relieving RA symptoms.
Collapse
Affiliation(s)
- Yan Su
- Microbial Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-Si 56212, South Korea; Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju 54896, South Korea
| | - Yunjon Han
- Microbial Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-Si 56212, South Korea
| | - Hack Sun Choi
- Department of Biochemistry & Molecular Biology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Gil-Yong Lee
- Healthcare Technology Institute, Kolon Advanced Research Center, 110 Magokdong-ro, Seoul 07793, South Korea
| | - Hee Won Cho
- Healthcare Technology Institute, Kolon Advanced Research Center, 110 Magokdong-ro, Seoul 07793, South Korea
| | - Heonsik Choi
- Healthcare Technology Institute, Kolon Advanced Research Center, 110 Magokdong-ro, Seoul 07793, South Korea
| | - Jong Hyun Choi
- Microbial Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-Si 56212, South Korea
| | - Yong-Suk Jang
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju 54896, South Korea.
| | - Jeong-Woo Seo
- Microbial Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-Si 56212, South Korea.
| |
Collapse
|
8
|
Swinkels D, Kocherlakota S, Das Y, Dane AD, Wever EJM, Vaz FM, Bazan NG, Van Veldhoven PP, Baes M. DHA Shortage Causes the Early Degeneration of Photoreceptors and RPE in Mice With Peroxisomal β-Oxidation Deficiency. Invest Ophthalmol Vis Sci 2023; 64:10. [PMID: 37934161 PMCID: PMC10631513 DOI: 10.1167/iovs.64.14.10] [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: 05/23/2023] [Accepted: 09/06/2023] [Indexed: 11/08/2023] Open
Abstract
Purpose Patients deficient in peroxisomal β-oxidation, which is essential for the synthesis of docosahexaenoic acid (DHA, C22:6n-3) and breakdown of very-long-chain polyunsaturated fatty acids (VLC-PUFAs), both important components of photoreceptor outer segments, develop retinopathy present with retinopathy. The representative mouse model lacking the central enzyme of this pathway, multifunctional protein 2 (Mfp2-/-), also show early-onset retinal decay and cell-autonomous retinal pigment epithelium (RPE) degeneration, accompanied by reduced plasma and retinal DHA levels. In this study, we investigated whether DHA supplementation can rescue the retinal degeneration of Mfp2-/- mice. Methods Mfp2+/- breeding pairs and their offspring were fed a 0.12% DHA or control diet during gestation and lactation and until sacrifice. Offspring were analyzed for retinal function via electroretinograms and for lipid composition of neural retina and plasma with lipidome analysis and gas chromatography, respectively, and histologically using retinal sections and RPE flatmounts at the ages of 4, 8, and 16 weeks. Results DHA supplementation to Mfp2-/- mice restored retinal DHA levels and prevented photoreceptor shortening, death, and impaired functioning until 8 weeks. In addition, rescue of retinal DHA levels temporarily improved the ability of the RPE to phagocytose outer segments and delayed the RPE dedifferentiation. However, despite the initial rescue of retinal integrity, DHA supplementation could not prevent retinal degeneration at 16 weeks. Conclusions We reveal that the shortage of a systemic supply of DHA is pivotal for the early retinal degeneration in Mfp2-/- mice. Furthermore, we report that adequate retinal DHA levels are essential not only for photoreceptors but also for RPE homeostasis.
Collapse
Affiliation(s)
- Daniëlle Swinkels
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Sai Kocherlakota
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Yannick Das
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Adriaan D. Dane
- Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eric J. M. Wever
- Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Frédéric M. Vaz
- Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Inborn Errors of Metabolism, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Nicolas G. Bazan
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, Louisiana State University, New Orleans, Louisiana, United States
| | - Paul P. Van Veldhoven
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| |
Collapse
|
9
|
Lipidomics analysis in drug discovery and development. Curr Opin Chem Biol 2023; 72:102256. [PMID: 36586190 DOI: 10.1016/j.cbpa.2022.102256] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/30/2022]
Abstract
Despite being a relatively new addition to the Omics' landscape, lipidomics is increasingly being recognized as an important tool for the identification of druggable targets and biochemical markers. In this review we present recent advances of lipid analysis in drug discovery and development. We cover current state of the art technologies which are constantly evolving to meet demands in terms of sensitivity and selectivity. A careful selection of important examples is then provided, illustrating the versatility of lipidomics analysis in the drug discovery and development process. Integration of lipidomics with other omics', stem-cell technologies, and metabolic flux analysis will open new avenues for deciphering pathophysiological mechanisms and the discovery of novel targets and biomarkers.
Collapse
|
10
|
Shanbhag K, Sharma K, Kamat SS. Photoreactive bioorthogonal lipid probes and their applications in mammalian biology. RSC Chem Biol 2023; 4:37-46. [PMID: 36685253 PMCID: PMC9811504 DOI: 10.1039/d2cb00174h] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
Lipids are an important class of biological molecules that possess many critical physiological functions, which enable the optimal survival of all organisms, including humans. While the role of lipids in the formation of biological cellular membranes and as a source of energy is fairly well understood, the cellular signalling pathways that lipids modulate in mammals are, in comparison, poorly characterized mechanistically and/or largely unknown. In an effort to dissect these mammalian cellular pathways regulated by signalling lipids and map hitherto unknown protein-lipid interactions, the last two decades have seen tremendous progress in the development of multifunctional lipid probes that, in conjunction with well-established bioorthogonal chemistries and chemoproteomics platforms, has almost exponentially expanded our knowledge in this field. In this review, we focus on the various photoreactive bioorthogonal lipid probes described in the literature, and briefly summarize the different photo-crosslinking groups and bioorthogonal chemistries used by them. Furthermore, we report specific case examples of such photoreactive bioorthogonal lipid probes, and discuss the new biological pathways and insights that have emerged from their use through chemoproteomics in mammalian cells. Finally, we highlight the challenges associated with the use of lipid probes in biological systems, and highlight their importance in the discovery and mechanistic understanding of lipid signalling pathways in the years to come.
Collapse
Affiliation(s)
- Karthik Shanbhag
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan Pune 411008 Maharashtra India
| | - Kavita Sharma
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan Pune 411008 Maharashtra India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan Pune 411008 Maharashtra India
| |
Collapse
|
11
|
Ge J, Du S, Yao SQ. Bifunctional Lipid-Derived Affinity-Based Probes (A fBPs) for Analysis of Lipid-Protein Interactome. Acc Chem Res 2022; 55:3663-3674. [PMID: 36484537 DOI: 10.1021/acs.accounts.2c00593] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although lipids are not genetically encoded, they are fundamental building blocks of cell membranes and essential components of cell metabolites. Lipids regulate various biological processes, including energy storage, membrane trafficking, signal transduction, and protein secretion; therefore, their metabolic imbalances cause many diseases. Approximately 47 000 lipid species with diverse structures have been identified, but little is known about their crucial roles in cellular systems. Particularly the structural, metabolic, and signaling functions of lipids often arise from interactions with proteins. Lipids attach to proteins not only by covalent bonds but also through noncovalent interactions, which also influence protein functions and localization. Therefore, it is important to explore this lipid-protein "interactome" to understand its roles in health and disease, which may further provide insight for medicinal development. However, lipid structures are generally quite complicated, rendering the systematic characterization of lipid-protein interactions much more challenging.Chemoproteomics is a well-known chemical biology platform in which small-molecule chemical probes are utilized in combination with high-resolution, quantitative mass spectrometry to study protein-ligand interactions in living cells or organisms, and it has recently been applied to the study of protein-lipid interactions as well. The study of these complicated interactions has been advanced by the development of bifunctional lipid probes, which not only enable probes to form covalent cross-links with lipid-interacting proteins under UV irradiation, but are also capable of enriching these proteins through bioorthogonal reactions.In this Account, we will discuss recent developments in bifunctional lipid-derived, affinity-based probes (AfBP)s that have been developed to investigate lipid-protein interactions in live cell systems. First, we will give a brief introduction of fundamental techniques based on AfBPs which are related to lipid research. Then, we will focus on three aspects, including probes developed on the basis of lipidation, lipid-derived probes with different modification positions (e.g., hydrophobic or hydrophilic parts of a lipid), and, finally, in situ biosynthesis of probes through intrinsic metabolic pathways by using chemically modified building blocks. We will present some case studies to describe these probes' design principles and cellular applications. At the end, we will also highlight key limitations of current approaches so as to provide inspirations for future improvement. The lipid probes that have been constructed are only the tip of the iceberg, and there are still plenty of lipid species that have yet to be explored. We anticipate that AfBP-based chemoproteomics and its further advancement will pave the way for a deep understanding of lipid-protein interactions in the future.
Collapse
Affiliation(s)
- Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore
| |
Collapse
|