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Chang JK, Teo G, Pewzner-Jung Y, Cuthbertson DJ, Futerman AH, Wenk MR, Choi H, Torta F. Author Correction: Q-RAI data-independent acquisition for lipidomic quantitative profiling. Sci Rep 2024; 14:4908. [PMID: 38418522 PMCID: PMC10902349 DOI: 10.1038/s41598-024-55396-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024] Open
Affiliation(s)
- Jing Kai Chang
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Guoshou Teo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yael Pewzner-Jung
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Markus R Wenk
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hyungwon Choi
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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Bisgaard LS, Christensen PM, Oh J, Torta F, Füchtbauer EM, Nielsen LB, Christoffersen C. Kidney derived apolipoprotein M and its role in acute kidney injury. Front Pharmacol 2024; 15:1328259. [PMID: 38313311 PMCID: PMC10834784 DOI: 10.3389/fphar.2024.1328259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024] Open
Abstract
Aim: Apolipoprotein M (apoM) is mainly expressed in liver and in proximal tubular epithelial cells in the kidney. In plasma, apoM associates with HDL particles via a retained signal peptide and carries sphingosine-1-phosphate (S1P), a small bioactive lipid. ApoM is undetectable in urine from healthy individuals but lack of megalin receptors in proximal tubuli cells induces loss of apoM into the urine. Besides this, very little is known about kidney-derived apoM. The aim of this study was to address the role of apoM in kidney biology and in acute kidney injury. Methods: A novel kidney-specific human apoM transgenic mouse model (RPTEC-hapoMTG) was generated and subjected to either cisplatin or ischemia/reperfusion injury. Further, a stable transfection of HK-2 cells overexpressing human apoM (HK-2-hapoMTG) was developed to study the pattern of apoM secretion in proximal tubuli cells. Results: Human apoM was present in plasma from RPTEC-hapoMTG mice (mean 0.18 μM), with a significant increase in plasma S1P levels. In vitro apoM was secreted to both the apical (urine) and basolateral (blood) compartment from proximal tubular epithelial cells. However, no differences in kidney injury score was seen between RPTEC-hapoMTG and wild type (WT) mice upon kidney injury. Further, gene expression of inflammatory markers (i.e., IL6, MCP-1) was similar upon ischemia/reperfusion injury. Conclusion: Our study suggests that kidney-derived apoM is secreted to plasma, supporting a role for apoM in sequestering molecules from excretion in urine. However, overexpression of human apoM in the kidney did not protect against acute kidney injury.
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Affiliation(s)
- Line S. Bisgaard
- Department of Clinical Biochemistry, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pernille M. Christensen
- Department of Clinical Biochemistry, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeongah Oh
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Lars Bo Nielsen
- The Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
| | - Christina Christoffersen
- Department of Clinical Biochemistry, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
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Chua XY, Torta F, Chong JR, Venketasubramanian N, Hilal S, Wenk MR, Chen CP, Arumugam TV, Herr DR, Lai MKP. Lipidomics profiling reveals distinct patterns of plasma sphingolipid alterations in Alzheimer's disease and vascular dementia. Alzheimers Res Ther 2023; 15:214. [PMID: 38087395 PMCID: PMC10714620 DOI: 10.1186/s13195-023-01359-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) and vascular dementia (VaD) are two of the commonest causes of dementia in the elderly. Of the myriad biomolecules implicated in dementia pathogenesis, sphingolipids have attracted relatively scant research attention despite their known involvement in multiple pathophysiological processes. The potential utility of peripheral sphingolipids as biomarkers in dementia cohorts with high concomitance of cerebrovascular diseases is also unclear. METHODS Using a lipidomics platform, we performed a case-control study of plasma sphingolipids in a prospectively assessed cohort of 526 participants (non-cognitively impaired, NCI = 93, cognitively impaired = 217, AD = 166, VaD = 50) using a lipidomics platform. RESULTS Distinct patterns of sphingolipid alterations were found in AD and VaD, namely an upregulation of d18:1 species in AD compared to downregulation of d16:1 species in VaD. In particular, GM3 d18:1/16:0 and GM3 d18:1/24:1 showed the strongest positive associations with AD. Furthermore, evaluation of sphingolipids panels showed specific combinations with higher sensitivity and specificity for classification of AD (Cer d16:1/24:0. Cer d18:1/16:0, GM3 d16:1/22:0, GM3 d18:1/16:0, SM d16:1/22:0, HexCer d18:1/18:0) and VAD (Cer d16:1/24:0, Cer d18:1/16:0, Hex2Cer d16:1/16:0, HexCer d18:1/18:0, SM d16:1/16:0, SM d16:1/20:0, SM d18:2/22:0) compared to NCI. CONCLUSIONS AD and VaD are associated with distinct changes of plasma sphingolipids, warranting further studies into underlying pathophysiological mechanisms and assessments of their potential utility as dementia biomarkers and therapeutic targets.
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Affiliation(s)
- Xin Ying Chua
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joyce R Chong
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Memory, Aging and Cognition Centre, National University Health System, Singapore, Singapore
| | | | - Saima Hilal
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Memory, Aging and Cognition Centre, National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Memory, Aging and Cognition Centre, National University Health System, Singapore, Singapore
| | - Thiruma V Arumugam
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, Australia
| | - Deron R Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Memory, Aging and Cognition Centre, National University Health System, Singapore, Singapore.
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4
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Chang JK, Teo G, Pewzner-Jung Y, Cuthbertson DJ, Futerman AH, Wenk MR, Choi H, Torta F. Q-RAI data-independent acquisition for lipidomic quantitative profiling. Sci Rep 2023; 13:19281. [PMID: 37935746 PMCID: PMC10630469 DOI: 10.1038/s41598-023-46312-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Untargeted lipidomics has been increasingly adopted for hypothesis generation in a biological context or discovery of disease biomarkers. Most of the current liquid chromatography mass spectrometry (LC-MS) based untargeted methodologies utilize a data dependent acquisition (DDA) approach in pooled samples for identification and MS-only acquisition for semi-quantification in individual samples. In this study, we present for the first time an untargeted lipidomic workflow that makes use of the newly implemented Quadrupole Resolved All-Ions (Q-RAI) acquisition function on the Agilent 6546 quadrupole time-of-flight (Q-TOF) mass spectrometer to acquire MS2 spectra in data independent acquisition (DIA) mode. This is followed by data processing and analysis on MetaboKit, a software enabling DDA-based spectral library construction and extraction of MS1 and MS2 peak areas, for reproducible identification and quantification of lipids in DIA analysis. This workflow was tested on lipid extracts from human plasma and showed quantification at MS1 and MS2 levels comparable to multiple reaction monitoring (MRM) targeted analysis of the same samples. Analysis of serum from Ceramide Synthase 2 (CerS2) null mice using the Q-RAI DIA workflow identified 88 lipid species significantly different between CerS2 null and wild type mice, including well-characterized changes previously associated with this phenotype. Our results show the Q-RAI DIA as a reliable option to perform simultaneous identification and reproducible relative quantification of lipids in exploratory biological studies.
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Affiliation(s)
- Jing Kai Chang
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Guoshou Teo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yael Pewzner-Jung
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Markus R Wenk
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hyungwon Choi
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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5
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Park DS, Kozaki T, Tiwari SK, Moreira M, Khalilnezhad A, Torta F, Olivié N, Thiam CH, Liani O, Silvin A, Phoo WW, Gao L, Triebl A, Tham WK, Gonçalves L, Kong WT, Raman S, Zhang XM, Dunsmore G, Dutertre CA, Lee S, Ong JM, Balachander A, Khalilnezhad S, Lum J, Duan K, Lim ZM, Tan L, Low I, Utami KH, Yeo XY, Di Tommaso S, Dupuy JW, Varga B, Karadottir RT, Madathummal MC, Bonne I, Malleret B, Binte ZY, Wei Da N, Tan Y, Wong WJ, Zhang J, Chen J, Sobota RM, Howland SW, Ng LG, Saltel F, Castel D, Grill J, Minard V, Albani S, Chan JKY, Thion MS, Jung SY, Wenk MR, Pouladi MA, Pasqualini C, Angeli V, Cexus ONF, Ginhoux F. iPS-cell-derived microglia promote brain organoid maturation via cholesterol transfer. Nature 2023; 623:397-405. [PMID: 37914940 DOI: 10.1038/s41586-023-06713-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Microglia are specialized brain-resident macrophages that arise from primitive macrophages colonizing the embryonic brain1. Microglia contribute to multiple aspects of brain development, but their precise roles in the early human brain remain poorly understood owing to limited access to relevant tissues2-6. The generation of brain organoids from human induced pluripotent stem cells recapitulates some key features of human embryonic brain development7-10. However, current approaches do not incorporate microglia or address their role in organoid maturation11-21. Here we generated microglia-sufficient brain organoids by coculturing brain organoids with primitive-like macrophages generated from the same human induced pluripotent stem cells (iMac)22. In organoid cocultures, iMac differentiated into cells with microglia-like phenotypes and functions (iMicro) and modulated neuronal progenitor cell (NPC) differentiation, limiting NPC proliferation and promoting axonogenesis. Mechanistically, iMicro contained high levels of PLIN2+ lipid droplets that exported cholesterol and its esters, which were taken up by NPCs in the organoids. We also detected PLIN2+ lipid droplet-loaded microglia in mouse and human embryonic brains. Overall, our approach substantially advances current human brain organoid approaches by incorporating microglial cells, as illustrated by the discovery of a key pathway of lipid-mediated crosstalk between microglia and NPCs that leads to improved neurogenesis.
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Affiliation(s)
- Dong Shin Park
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tatsuya Kozaki
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Satish Kumar Tiwari
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Marco Moreira
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France
| | - Ahad Khalilnezhad
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Nicolas Olivié
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Chung Hwee Thiam
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Oniko Liani
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Aymeric Silvin
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France
| | - Wint Wint Phoo
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Liang Gao
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Alexander Triebl
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Wai Kin Tham
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | | | - Wan Ting Kong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sethi Raman
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Xiao Meng Zhang
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Garett Dunsmore
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France
| | - Charles Antoine Dutertre
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France
| | - Salanne Lee
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Jia Min Ong
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Akhila Balachander
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Shabnam Khalilnezhad
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Kaibo Duan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Ze Ming Lim
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Leonard Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Ivy Low
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Kagistia Hana Utami
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research, Singapore, Singapore
| | - Xin Yi Yeo
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore, Singapore
| | | | | | - Balazs Varga
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute and Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ragnhildur Thora Karadottir
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute and Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mufeeda Changaramvally Madathummal
- A*STAR Microscopy Platform Electron Microscopy, Research Support Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Isabelle Bonne
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- A*STAR Microscopy Platform Electron Microscopy, Research Support Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zainab Yasin Binte
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Ngan Wei Da
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Yingrou Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Wei Jie Wong
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinqiu Zhang
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research, Singapore, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Shanshan W Howland
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - David Castel
- INSERM U981, Molecular Predictors and New Targets in Oncology & Département de Cancérologie de l'Enfant et de l'Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jacques Grill
- INSERM U981, Molecular Predictors and New Targets in Oncology & Département de Cancérologie de l'Enfant et de l'Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Jerry K Y Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Morgane Sonia Thion
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Sang Yong Jung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medical Science, College of Medicine, CHA University, Seongnam, Republic of Korea
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Mahmoud A Pouladi
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | | | - Veronique Angeli
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Olivier N F Cexus
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore, Singapore
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif, France.
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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6
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Chin CF, Galam DL, Gao L, Tan BC, Wong BH, Chua GL, Loke RY, Lim YC, Wenk MR, Lim MS, Leow WQ, Goh GB, Torta F, Silver DL. Blood-derived lysophospholipid sustains hepatic phospholipids and fat storage necessary for hepatoprotection in overnutrition. J Clin Invest 2023; 133:e171267. [PMID: 37463052 PMCID: PMC10471173 DOI: 10.1172/jci171267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
The liver has a high demand for phosphatidylcholine (PC), particularly in overnutrition, where reduced phospholipid levels have been implicated in the development of nonalcoholic fatty liver disease (NAFLD). Whether other pathways exist in addition to de novo PC synthesis that contribute to hepatic PC pools remains unknown. Here, we identified the lysophosphatidylcholine (LPC) transporter major facilitator superfamily domain containing 2A (Mfsd2a) as critical for maintaining hepatic phospholipid pools. Hepatic Mfsd2a expression was induced in patients having NAFLD and in mice in response to dietary fat via glucocorticoid receptor action. Mfsd2a liver-specific deficiency in mice (L2aKO) led to a robust nonalcoholic steatohepatitis-like (NASH-like) phenotype within just 2 weeks of dietary fat challenge associated with reduced hepatic phospholipids containing linoleic acid. Reducing dietary choline intake in L2aKO mice exacerbated liver pathology and deficiency of liver phospholipids containing polyunsaturated fatty acids (PUFAs). Treating hepatocytes with LPCs containing oleate and linoleate, two abundant blood-derived LPCs, specifically induced lipid droplet biogenesis and contributed to phospholipid pools, while LPC containing the omega-3 fatty acid docosahexaenoic acid (DHA) promoted lipid droplet formation and suppressed lipogenesis. This study revealed that PUFA-containing LPCs drive hepatic lipid droplet formation, suppress lipogenesis, and sustain hepatic phospholipid pools - processes that are critical for protecting the liver from excess dietary fat.
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Affiliation(s)
- Cheen Fei Chin
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Dwight L.A. Galam
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Liang Gao
- Singapore Lipidomics Incubator, Life Sciences Institute and
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bryan C. Tan
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Bernice H. Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Geok-Lin Chua
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Randy Y.J. Loke
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Yen Ching Lim
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute and
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Miao-Shan Lim
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore
| | - Wei-Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, and
| | - George B.B. Goh
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore
- Medicine Academic Clinical Program, Duke-NUS Medical School, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute and
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David L. Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
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7
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Loke RYJ, Chin CF, Liang G, Wong BH, Galam DLA, Tan BC, Chua GL, Minegishi S, Morisawa N, Sidorov I, Heijs B, Titze J, Wenk MR, Torta F, Silver DL. Mfsd2a-mediated lysolipid transport is important for renal recovery after acute kidney injury. J Lipid Res 2023; 64:100416. [PMID: 37467896 PMCID: PMC10424216 DOI: 10.1016/j.jlr.2023.100416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Acute kidney injury (AKI) is a global public health concern with high mortality and morbidity. In ischemic-reperfusion injury (IRI), a main cause of AKI, the brush border membrane of S3 proximal tubules (PT) is lost to the tubular lumen. How injured tubules reconstitute lost membrane lipids during renal recovery is not known. Here, we identified Mfsd2a, a sodium-dependent lysophosphatidylcholine (LPC) transporter, to be expressed specifically in the basolateral membrane of S3 PT. Using an in vivo activity probe for Mfsd2a, transport activity was found to be specific to the S3 PT. Mice with haploinsufficiency of Mfsd2a exhibited delayed recovery of renal function after acute IRI, with depressed urine osmolality and elevated levels of histological markers of damage, fibrosis, and inflammation, findings corroborated by transcriptomic analysis. Lipidomics revealed a deficiency in docosahexaenoic acid (DHA) containing phospholipids in Mfsd2a haploinsufficiency. Treatment of Mfsd2a haploinsufficient mice with LPC-DHA improved renal function and reduced markers of injury, fibrosis, and inflammation. Additionally, LPC-DHA treatment restored S3 brush border membrane architecture and normalized DHA-containing phospholipid content. These findings indicate that Mfsd2a-mediated transport of LPC-DHA is limiting for renal recovery after AKI and suggest that LPC-DHA could be a promising dietary supplement for improving recovery following AKI.
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Affiliation(s)
- Randy Y J Loke
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Cheen Fei Chin
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Gao Liang
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore
| | - Bernice H Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Dwight L A Galam
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Bryan C Tan
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Geok-Lin Chua
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Shintaro Minegishi
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Norihiko Morisawa
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Iulia Sidorov
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands
| | - Bram Heijs
- Center of Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands
| | - Jens Titze
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore
| | - David L Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore.
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8
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Sengottuvel V, Hota M, Oh J, Galam DL, Wong BH, Wenk MR, Ghosh S, Torta F, Silver DL. Deficiency in the omega-3 lysolipid transporter Mfsd2a leads to aberrant oligodendrocyte lineage development and hypomyelination. J Clin Invest 2023:164118. [PMID: 37104036 DOI: 10.1172/jci164118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Patients with Autosomal Recessive Microcephaly 15 caused by deficiency in the sodium-dependent lysophosphatidylcholine (LPC) transporter Major Facilitator Superfamily Domain containing 2a (Mfsd2a) present with both microcephaly and hypomyelination, suggesting an important role of LPC uptake by oligodendrocytes in the process of myelination. Here, we demonstrate that Mfsd2a is specifically expressed in oligodendrocyte precursor cells (OPC) and is critical for oligodendrocyte development. Single cell sequencing of the oligodendrocyte lineage revealed that OPCs from OPC-specific Mfsd2a KO mice (2aOKO) underwent precocious differentiation into immature oligodendrocytes (iOLs) and impaired maturation into myelinating oligodendrocytes, correlating with postnatal brain hypomyelination. 2aOKO mice did not exhibit microcephaly, consistent with microcephaly being consequential to absence of LPC uptake at the blood-brain barrier and not from deficiency in OPCs. Lipidomic analysis showed that OPCs and iOLs from 2aOKO mice had significantly decreased phospholipids containing omega-3 fatty acids with an opposite increase in unsaturated fatty acids, that latter being products of de novo synthesis governed by Srebp-1. RNA sequencing indicated activation of the Srebp-1 pathway and defective expression of regulators of oligodendrocyte development. Taken together, these findings indicate that the transport of LPCs by Mfsd2a in OPCs is important for maintaining OPC cell state to regulate postnatal brain myelination.
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Affiliation(s)
- Vetrivel Sengottuvel
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Monalisa Hota
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Jeongah Oh
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Dwight L Galam
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Bernice H Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Markus R Wenk
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Sujoy Ghosh
- Centre for Computational Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Federico Torta
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - David L Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
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9
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Chua GL, Tan BC, Loke RYJ, He M, Chin CF, Wong BH, Kuk ACY, Ding M, Wenk MR, Guan L, Torta F, Silver DL. Mfsd2a utilizes a flippase mechanism to mediate omega-3 fatty acid lysolipid transport. Proc Natl Acad Sci U S A 2023; 120:e2215290120. [PMID: 36848557 PMCID: PMC10013850 DOI: 10.1073/pnas.2215290120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
Major Facilitator Superfamily Domain containing 2a (Mfsd2a) is a sodium-dependent lysophosphatidylcholine (LPC) transporter expressed at the blood-brain barrier that constitutes the main pathway by which the brain obtains omega-3 fatty acids, such as docosahexanoic acid. Mfsd2a deficiency in humans results in severe microcephaly, underscoring the importance of LPC transport by Mfsd2a for brain development. Biochemical studies and recent cryo-electron microscopy (cryo-EM) structures of Mfsd2a bound to LPC suggest that Mfsd2a transports LPC via an alternating access mechanism between outward-facing and inward-facing conformational states in which the LPC inverts during transport between the outer and inner leaflet of a membrane. However, direct biochemical evidence of flippase activity by Mfsd2a has not been demonstrated and it is not understood how Mfsd2a could invert LPC between the outer and inner leaflet of the membrane in a sodium-dependent manner. Here, we established a unique in vitro assay using recombinant Mfsd2a reconstituted in liposomes that exploits the ability of Mfsd2a to transport lysophosphatidylserine (LPS) coupled with a small molecule LPS binding fluorophore that allowed for monitoring of directional flipping of the LPS headgroup from the outer to the inner liposome membrane. Using this assay, we demonstrate that Mfsd2a flips LPS from the outer to the inner leaflet of a membrane bilayer in a sodium-dependent manner. Furthermore, using cryo-EM structures as guides together with mutagenesis and a cell-based transport assay, we identify amino acid residues important for Mfsd2a activity that likely constitute substrate interaction domains. These studies provide direct biochemical evidence that Mfsd2a functions as a lysolipid flippase.
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Affiliation(s)
- Geok-Lin Chua
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Bryan C. Tan
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Randy Y. J. Loke
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Menglan He
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Cheen-Fei Chin
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Bernice H. Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Alvin C. Y. Kuk
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Mei Ding
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117596, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117596, Singapore
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX79430
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117596, Singapore
| | - David L. Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore169857, Singapore
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10
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Koh HW, Pilbrow AP, Tan SH, Zhao Q, Benke PI, Burla B, Torta F, Pickering JW, Troughton R, Pemberton C, Soo WM, Ling LH, Doughty RN, Choi H, Wenk MR, Richards AM, Chan MY. An integrated signature of extracellular matrix proteins and a diastolic function imaging parameter predicts post-MI long-term outcomes. Front Cardiovasc Med 2023; 10:1123682. [PMID: 37123479 PMCID: PMC10132266 DOI: 10.3389/fcvm.2023.1123682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
Background Patients suffering from acute myocardial infarction (AMI) are at risk of secondary outcomes including major adverse cardiovascular events (MACE) and heart failure (HF). Comprehensive molecular phenotyping and cardiac imaging during the post-discharge time window may provide cues for risk stratification for the outcomes. Materials and methods In a prospective AMI cohort in New Zealand (N = 464), we measured plasma proteins and lipids 30 days after hospital discharge and inferred a unified partial correlation network with echocardiographic variables and established clinical biomarkers (creatinine, c-reactive protein, cardiac troponin I and natriuretic peptides). Using a network-based data integration approach (iOmicsPASS+), we identified predictive signatures of long-term secondary outcomes based on plasma protein, lipid, imaging markers and clinical biomarkers and assessed the prognostic potential in an independent cohort from Singapore (N = 190). Results The post-discharge levels of plasma proteins and lipids showed strong correlations within each molecular type, reflecting concerted homeostatic regulation after primary MI events. However, the two molecular types were largely independent with distinct correlation structures with established prognostic imaging parameters and clinical biomarkers. To deal with massively correlated predictive features, we used iOmicsPASS + to identify subnetwork signatures of 211 and 189 data features (nodes) predictive of MACE and HF events, respectively (160 overlapping). The predictive features were primarily imaging parameters, including left ventricular and atrial parameters, tissue Doppler parameters, and proteins involved in extracellular matrix (ECM) organization, cell differentiation, chemotaxis, and inflammation. The network signatures contained plasma protein pairs with area-under-the-curve (AUC) values up to 0.74 for HF prediction in the validation cohort, but the pair of NT-proBNP and fibulin-3 (EFEMP1) was the best predictor (AUC = 0.80). This suggests that there were a handful of plasma proteins with mechanistic and functional roles in predisposing patients to the secondary outcomes, although they may be weaker prognostic markers than natriuretic peptides individually. Among those, the diastolic function parameter (E/e' - an indicator of left ventricular filling pressure) and two ECM proteins, EFEMP1 and follistatin-like 3 (FSTL3) showed comparable performance to NT-proBNP and outperformed left ventricular measures as benchmark prognostic factors for post-MI HF. Conclusion Post-discharge levels of E/e', EFEMP1 and FSTL3 are promising complementary markers of secondary adverse outcomes in AMI patients.
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Affiliation(s)
- Hiromi W.L. Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anna P. Pilbrow
- Department of Medicine, Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Sock Hwee Tan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National University Heart Centre, National University Health System, Singapore, Singapore
| | - Qing Zhao
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peter I. Benke
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - John W. Pickering
- Department of Medicine, Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Richard Troughton
- Department of Medicine, Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Christopher Pemberton
- Department of Medicine, Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Wern-Miin Soo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National University Heart Centre, National University Health System, Singapore, Singapore
| | - Lieng Hsi Ling
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National University Heart Centre, National University Health System, Singapore, Singapore
| | - Robert N. Doughty
- Heart Health Research Group, University of Auckland, Auckland, New Zealand
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - A. Mark Richards
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
- National University Heart Centre, National University Health System, Singapore, Singapore
- Correspondence: Mark Richards Mark Chan
| | - Mark Y. Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- National University Heart Centre, National University Health System, Singapore, Singapore
- Correspondence: Mark Richards Mark Chan
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11
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Abstract
In recent decades, mass spectrometry-based lipidomics has provided a fertile environment for scientific investigations of biochemical and mechanistic processes in biological systems. Notably, this approach has been used to characterize physiological and pathological processes relevant to the central nervous system by identifying changes in the sphingolipid content in the brain, cerebral spinal fluid, and blood plasma. However, despite a preponderance of studies identifying correlations between specific lipids and disease progression, this powerful resource has not yet substantively translated into clinically useful diagnostic assays. Part of this gap may be explained by insufficient depth of the lipidomic profiles in many studies, by lab-to-lab inconsistencies in methodology, and a lack of absolute quantification. These issues limit the identification of specific molecular species and the harmonization of results across independent studies. In this chapter, we contextualize these issues with recent reports identifying correlations between brain lipids and neurological diseases, and we describe the workflow our group has optimized for analysis of the blood plasma sphingolipidome, adapted to the characterization of the human brain tissue.
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Affiliation(s)
- Xin Ying Chua
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Memory Aging and Cognition Centre, Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ryan Huang
- Canyon Crest Academy, San Diego, CA, USA
| | - Deron Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Memory Aging and Cognition Centre, Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Markus R Wenk
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore, Singapore
| | - Federico Torta
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore, Singapore.
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore, Singapore.
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12
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Wang J, Liu JJ, Gurung RL, Liu S, Lee J, M Y, Ang K, Shao YM, Tang JIS, Benke PI, Torta F, Wenk MR, Tavintharan S, Tang WE, Sum CF, Lim SC. Clinical variable-based cluster analysis identifies novel subgroups with a distinct genetic signature, lipidomic pattern and cardio-renal risks in Asian patients with recent-onset type 2 diabetes. Diabetologia 2022; 65:2146-2156. [PMID: 35763031 PMCID: PMC9630229 DOI: 10.1007/s00125-022-05741-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 01/11/2023]
Abstract
AIMS/HYPOTHESIS We sought to subtype South East Asian patients with type 2 diabetes by de novo cluster analysis on clinical variables, and to determine whether the novel subgroups carry distinct genetic and lipidomic features as well as differential cardio-renal risks. METHODS Analysis by k-means algorithm was performed in 687 participants with recent-onset diabetes in Singapore. Genetic risk for beta cell dysfunction was assessed by polygenic risk score. We used a discovery-validation approach for the lipidomics study. Risks for cardio-renal complications were studied by survival analysis. RESULTS Cluster analysis identified three novel diabetic subgroups, i.e. mild obesity-related diabetes (MOD, 45%), mild age-related diabetes with insulin insufficiency (MARD-II, 36%) and severe insulin-resistant diabetes with relative insulin insufficiency (SIRD-RII, 19%). Compared with the MOD subgroup, MARD-II had a higher polygenic risk score for beta cell dysfunction. The SIRD-RII subgroup had higher levels of sphingolipids (ceramides and sphingomyelins) and glycerophospholipids (phosphatidylethanolamine and phosphatidylcholine), whereas the MARD-II subgroup had lower levels of sphingolipids and glycerophospholipids but higher levels of lysophosphatidylcholines. Over a median of 7.3 years follow-up, the SIRD-RII subgroup had the highest risks for incident heart failure and progressive kidney disease, while the MARD-II subgroup had moderately elevated risk for kidney disease progression. CONCLUSIONS/INTERPRETATION Cluster analysis on clinical variables identified novel subgroups with distinct genetic, lipidomic signatures and varying cardio-renal risks in South East Asian participants with type 2 diabetes. Our study suggests that this easily actionable approach may be adapted in other ethnic populations to stratify the heterogeneous type 2 diabetes population for precision medicine.
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Affiliation(s)
- Jiexun Wang
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Jian-Jun Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Resham L Gurung
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Sylvia Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Janus Lee
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Yiamunaa M
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Keven Ang
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Yi Ming Shao
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Justin I-Shing Tang
- Department of Medicine, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Peter I Benke
- Lipidomics Incubator, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Federico Torta
- Lipidomics Incubator, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Markus R Wenk
- Lipidomics Incubator, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | | | - Wern Ee Tang
- National Healthcare Group Polyclinic, Singapore, Republic of Singapore
| | - Chee Fang Sum
- Diabetes Centre, Admiralty Medical Centre, Singapore, Republic of Singapore
| | - Su Chi Lim
- Diabetes Centre, Admiralty Medical Centre, Singapore, Republic of Singapore.
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Republic of Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
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13
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Wang J, Liu JJ, Gurung RL, Liu S, Lee J, Yiamunaa M, Ang K, Shao YM, Tang JIS, Benke PI, Torta F, Wenk MR, Tavintharan S, Tang WE, Sum CF, Lim SC. Correction: Clinical variable-based cluster analysis identifies novel subgroups with a distinct genetic signature, lipidomic pattern and cardio-renal risks in Asian patients with recent-onset type 2 diabetes. Diabetologia 2022; 65:2176. [PMID: 36069997 PMCID: PMC9630397 DOI: 10.1007/s00125-022-05783-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiexun Wang
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Jian-Jun Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Resham L Gurung
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Sylvia Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Janus Lee
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - M Yiamunaa
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Keven Ang
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Yi Ming Shao
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Justin I-Shing Tang
- Department of Medicine, Khoo Teck Puat Hospital, Singapore, Republic of Singapore
| | - Peter I Benke
- Lipidomics Incubator, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Federico Torta
- Lipidomics Incubator, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Markus R Wenk
- Lipidomics Incubator, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | | | - Wern Ee Tang
- National Healthcare Group Polyclinic, Singapore, Republic of Singapore
| | - Chee Fang Sum
- Diabetes Centre, Admiralty Medical Centre, Singapore, Republic of Singapore
| | - Su Chi Lim
- Diabetes Centre, Admiralty Medical Centre, Singapore, Republic of Singapore.
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Republic of Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
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14
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Stephenson MC, Krishna L, Pannir Selvan RM, Tai YK, Kit Wong CJ, Yin JN, Toh SJ, Torta F, Triebl A, Fröhlich J, Beyer C, Li JZ, Tan SS, Wong CK, Chinnasamy D, Pakkiri LS, Lee Drum C, Wenk MR, Totman JJ, Franco-Obregón A. Magnetic field therapy enhances muscle mitochondrial bioenergetics and attenuates systemic ceramide levels following ACL reconstruction: Southeast Asian randomized-controlled pilot trial. J Orthop Translat 2022; 35:99-112. [PMID: 36262374 PMCID: PMC9574347 DOI: 10.1016/j.jot.2022.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/06/2022] Open
Abstract
Background Metabolic disruption commonly follows Anterior Cruciate Ligament Reconstruction (ACLR) surgery. Brief exposure to low amplitude and frequency pulsed electromagnetic fields (PEMFs) has been shown to promote in vitro and in vivo murine myogeneses via the activation of a calcium–mitochondrial axis conferring systemic metabolic adaptations. This randomized-controlled pilot trial sought to detect local changes in muscle structure and function using MRI, and systemic changes in metabolism using plasma biomarker analyses resulting from ACLR, with or without accompanying PEMF therapy. Methods 20 patients requiring ACLR were randomized into two groups either undergoing PEMF or sham exposure for 16 weeks following surgery. The operated thighs of 10 patients were exposed weekly to PEMFs (1 mT for 10 min) for 4 months following surgery. Another 10 patients were subjected to sham exposure and served as controls to allow assessment of the metabolic repercussions of ACLR and PEMF therapy. Blood samples were collected prior to surgery and at 16 weeks for plasma analyses. Magnetic resonance data were acquired at 1 and 16 weeks post-surgery using a Siemens 3T Tim Trio system. Phosphorus (31P) Magnetic Resonance Spectroscopy (MRS) was utilized to monitor changes in high-energy phosphate metabolism (inorganic phosphate (Pi), adenosine triphosphate (ATP) and phosphocreatine (PCr)) as well as markers of membrane synthesis and breakdown (phosphomonoesters (PME) and phosphodiester (PDE)). Quantitative Magnetization Transfer (qMT) imaging was used to elucidate changes in the underlying tissue structure, with T1-weighted and 2-point Dixon imaging used to calculate muscle volumes and muscle fat content. Results Improvements in markers of high-energy phosphate metabolism including reductions in ΔPi/ATP, Pi/PCr and (Pi + PCr)/ATP, and membrane kinetics, including reductions in PDE/ATP were detected in the PEMF-treated cohort relative to the control cohort at study termination. These were associated with reductions in the plasma levels of certain ceramides and lysophosphatidylcholine species. The plasma levels of biomarkers predictive of muscle regeneration and degeneration, including osteopontin and TNNT1, respectively, were improved, whilst changes in follistatin failed to achieve statistical significance. Liquid chromatography with tandem mass spectrometry revealed reductions in small molecule biomarkers of metabolic disruption, including cysteine, homocysteine, and methionine in the PEMF-treated cohort relative to the control cohort at study termination. Differences in measurements of force, muscle and fat volumes did not achieve statistical significance between the cohorts after 16 weeks post-ACLR. Conclusion The detected changes suggest improvements in systemic metabolism in the post-surgical PEMF-treated cohort that accords with previous preclinical murine studies. PEMF-based therapies may potentially serve as a manner to ameliorate post-surgery metabolic disruptions and warrant future examination in more adequately powered clinical trials. The Translational Potential of this Article Some degree of physical immobilisation must inevitably follow orthopaedic surgical intervention. The clinical paradox of such a scenario is that the regenerative potential of the muscle mitochondrial pool is silenced. The unmet need was hence a manner to maintain mitochondrial activation when movement is restricted and without producing potentially damaging mechanical stress. PEMF-based therapies may satisfy the requirement of non-invasively activating the requisite mitochondrial respiration when mobility is restricted for improved metabolic and regenerative recovery.
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Affiliation(s)
- Mary C. Stephenson
- Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Corresponding author. Centre for Translational MR Research, Yong Loo Lin School of Medicine, Tahir Foundation Building, 13-03, MD1, National University of Singapore, Singapore, 117549.
| | - Lingaraj Krishna
- Division of Sports Medicine and Surgery, Department of Orthopaedic Surgery, National University Hospital, National University Health System, Singapore
| | - Rina Malathi Pannir Selvan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,BioIonic Currents Electromagnetic Pulsing Systems Laboratory, BICEPS, National University of Singapore, Singapore
| | - Yee Kit Tai
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,BioIonic Currents Electromagnetic Pulsing Systems Laboratory, BICEPS, National University of Singapore, Singapore,Corresponding author. Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 8, 1E Kent Ridge Road, Singapore, 119228.
| | - Craig Jun Kit Wong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,BioIonic Currents Electromagnetic Pulsing Systems Laboratory, BICEPS, National University of Singapore, Singapore
| | - Jocelyn Naixin Yin
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,BioIonic Currents Electromagnetic Pulsing Systems Laboratory, BICEPS, National University of Singapore, Singapore
| | - Shi-Jie Toh
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,BioIonic Currents Electromagnetic Pulsing Systems Laboratory, BICEPS, National University of Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore,Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Alexander Triebl
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | | | - Christian Beyer
- Centre Suisse d'électronique et de Microtechnique, CSEM SA, Neuchatel, Switzerland
| | - Jing Ze Li
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sara S. Tan
- Division of Sports Medicine and Surgery, Department of Orthopaedic Surgery, National University Hospital, National University Health System, Singapore
| | - Chun-Kit Wong
- Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Duraimurugan Chinnasamy
- National University Hospital, Department of Rehabilitation Centre, National University Health System, Singapore
| | - Leroy Sivappiragasam Pakkiri
- Cardiovascular Research Institute (CVRI), National University Heart Centre Singapore (NUHCS), Singapore,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chester Lee Drum
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Cardiovascular Research Institute (CVRI), National University Heart Centre Singapore (NUHCS), Singapore,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore,Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - John J. Totman
- Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Academic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Alfredo Franco-Obregón
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,BioIonic Currents Electromagnetic Pulsing Systems Laboratory, BICEPS, National University of Singapore, Singapore,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Institute for Health Innovation & Technology, iHealthtech, National University of Singapore, Singapore,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore,Competence Center for Applied Biotechnology and Molecular Medicine, University of Zürich, Zürich, Switzerland,Corresponding author. Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, NUHS Tower Block Level 8, 1E Kent Ridge Road, Singapore, 119228.
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15
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Muralidharan S, Torta F, Lin MK, Olona A, Bagnati M, Moreno-Moral A, Ko JH, Ji S, Burla B, Wenk MR, Rodrigues HG, Petretto E, Behmoaras J. Immunolipidomics Reveals a Globoside Network During the Resolution of Pro-Inflammatory Response in Human Macrophages. Front Immunol 2022; 13:926220. [PMID: 35844525 PMCID: PMC9280915 DOI: 10.3389/fimmu.2022.926220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Toll-like receptor 4 (TLR4)-mediated changes in macrophages reshape intracellular lipid pools to coordinate an effective innate immune response. Although this has been previously well-studied in different model systems, it remains incompletely understood in primary human macrophages. Here we report time-dependent lipidomic and transcriptomic responses to lipopolysaccharide (LPS) in primary human macrophages from healthy donors. We grouped the variation of ~200 individual lipid species measured by LC-MS/MS into eight temporal clusters. Among all other lipids, glycosphingolipids (glycoSP) and cholesteryl esters (CE) showed a sharp increase during the resolution phase (between 8h or 16h post LPS). GlycoSP, belonging to the globoside family (Gb3 and Gb4), showed the greatest inter-individual variability among all lipids quantified. Integrative network analysis between GlycoSP/CE levels and genome-wide transcripts, identified Gb4 d18:1/16:0 and CE 20:4 association with subnetworks enriched for T cell receptor signaling (PDCD1, CD86, PTPRC, CD247, IFNG) and DC-SIGN signaling (RAF1, CD209), respectively. Our findings reveal Gb3 and Gb4 globosides as sphingolipids associated with the resolution phase of inflammatory response in human macrophages.
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Affiliation(s)
- Sneha Muralidharan
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,*Correspondence: Jacques Behmoaras, ; Federico Torta,
| | - Michelle K. Lin
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Antoni Olona
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore
| | - Marta Bagnati
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | - Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore
| | - Jeong-Hun Ko
- Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom
| | - Shanshan Ji
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore,Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hosana G. Rodrigues
- Laboratory of Nutrients and Tissue Repair, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore,MRC London Institute of Medical Sciences (LMC), Imperial College, London, United Kingdom,Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University, Nanjing, China
| | - Jacques Behmoaras
- Program in Cardiovascular and Metabolic Disorders (CVMD) and Center for Computational Biology (CCB), Duke NUS Graduate Medical School, Singapore, Singapore,Department of Immunology and Inflammation, Centre for Inflammatory Disease, Imperial College London, London, United Kingdom,*Correspondence: Jacques Behmoaras, ; Federico Torta,
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16
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Lippa KA, Aristizabal-Henao JJ, Beger RD, Bowden JA, Broeckling C, Beecher C, Clay Davis W, Dunn WB, Flores R, Goodacre R, Gouveia GJ, Harms AC, Hartung T, Jones CM, Lewis MR, Ntai I, Percy AJ, Raftery D, Schock TB, Sun J, Theodoridis G, Tayyari F, Torta F, Ulmer CZ, Wilson I, Ubhi BK. Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC). Metabolomics 2022; 18:24. [PMID: 35397018 PMCID: PMC8994740 DOI: 10.1007/s11306-021-01848-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022]
Abstract
INTRODUCTION The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for untargeted metabolomics research. OBJECTIVES This review aims to highlight current RMs, and methodologies used within untargeted metabolomics and lipidomics communities to ensure standardization of results obtained from data analysis, interpretation and cross-study, and cross-laboratory comparisons. The essence of the aims is also applicable to other 'omics areas that generate high dimensional data. RESULTS The potential for game-changing biochemical discoveries through mass spectrometry-based (MS) untargeted metabolomics and lipidomics are predicated on the evolution of more confident qualitative (and eventually quantitative) results from research laboratories. RMs are thus critical QC tools to be able to assure standardization, comparability, repeatability and reproducibility for untargeted data analysis, interpretation, to compare data within and across studies and across multiple laboratories. Standard operating procedures (SOPs) that promote, describe and exemplify the use of RMs will also improve QC for the metabolomics and lipidomics communities. CONCLUSIONS The application of RMs described in this review may significantly improve data quality to support metabolomics and lipidomics research. The continued development and deployment of new RMs, together with interlaboratory studies and educational outreach and training, will further promote sound QA practices in the community.
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Affiliation(s)
- Katrice A Lippa
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, 20899, USA
| | - Juan J Aristizabal-Henao
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
- BERG LLC, 500 Old Connecticut Path, Building B, 3rd Floor, Framingham, MA, 01710, USA
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, USA
| | - John A Bowden
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Corey Broeckling
- Analytical Resources Core: Bioanalysis and Omics Center, Colorado State University, Fort Collins, CO, 80523, USA
| | | | - W Clay Davis
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | - Warwick B Dunn
- School of Biosciences, Institute of Metabolism and Systems Research and Phenome Centre Birmingham, University of Birmingham, Birmingham, B15, 2TT, UK
| | - Roberto Flores
- Division of Program Coordination, Planning and Strategic Initiatives, Office of Nutrition Research, Office of the Director, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, UK
| | - Gonçalo J Gouveia
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Amy C Harms
- Biomedical Metabolomics Facility Leiden, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Thomas Hartung
- Bloomberg School of Public Health, Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Christina M Jones
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, 20899, USA
| | - Matthew R Lewis
- National Phenome Centre, Imperial College London, London, SW7 2AZ, UK
| | - Ioanna Ntai
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | - Andrew J Percy
- Cambridge Isotope Laboratories, Inc., Tewksbury, MA, 01876, USA
| | - Dan Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, 98109, USA
| | - Tracey B Schock
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, USA
| | | | - Fariba Tayyari
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Federico Torta
- Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Candice Z Ulmer
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, 30341, USA
| | - Ian Wilson
- Computational & Systems Medicine, Imperial College, Exhibition Rd, London, SW7 2AZ, UK
| | - Baljit K Ubhi
- MOBILion Systems Inc., 4 Hillman Drive Suite 130, Chadds Ford, PA, 19317, USA.
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17
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Zheng X, Ho QWC, Chua M, Stelmashenko O, Yeo XY, Muralidharan S, Torta F, Chew EGY, Lian MM, Foo JN, Jung S, Wong SH, Tan NS, Tong N, Rutter GA, Wenk MR, Silver DL, Berggren PO, Ali Y. Destabilization of β Cell FIT2 by saturated fatty acids alter lipid droplet numbers and contribute to ER stress and diabetes. Proc Natl Acad Sci U S A 2022; 119:e2113074119. [PMID: 35254894 PMCID: PMC8931238 DOI: 10.1073/pnas.2113074119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/29/2022] [Indexed: 02/05/2023] Open
Abstract
SignificanceWith obesity on the rise, there is a growing appreciation for intracellular lipid droplet (LD) regulation. Here, we show how saturated fatty acids (SFAs) reduce fat storage-inducing transmembrane protein 2 (FIT2)-facilitated, pancreatic β cell LD biogenesis, which in turn induces β cell dysfunction and death, leading to diabetes. This mechanism involves direct acylation of FIT2 cysteine residues, which then marks the FIT2 protein for endoplasmic reticulum (ER)-associated degradation. Loss of β cell FIT2 and LDs reduces insulin secretion, increases intracellular ceramides, stimulates ER stress, and exacerbates diet-induced diabetes in mice. While palmitate and stearate degrade FIT2, unsaturated fatty acids such as palmitoleate and oleate do not, results of which extend to nutrition and diabetes.
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Affiliation(s)
- Xiaofeng Zheng
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- Singapore Eye Research Institute, Singapore General Hospital, S168751, Singapore
- Department of Endocrinology and Metabolism, Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Qing Wei Calvin Ho
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
| | - Minni Chua
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
| | - Olga Stelmashenko
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- Singapore Eye Research Institute, Singapore General Hospital, S168751, Singapore
| | - Xin Yi Yeo
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, S138667, Singapore
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, S119228, Singapore
| | - Sneha Muralidharan
- Singapore Lipidomics Incubator, Department of Medicine, National University of Singapore, S117456, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, S117456, Singapore
| | - Elaine Guo Yan Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- Human Genetics, A*STAR, Genome Institute of Singapore, S138672, Singapore
| | - Michelle Mulan Lian
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- Human Genetics, A*STAR, Genome Institute of Singapore, S138672, Singapore
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- Human Genetics, A*STAR, Genome Institute of Singapore, S138672, Singapore
| | - Sangyong Jung
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, S138667, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, S117593, Singapore
| | - Sunny Hei Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, S637551, Singapore
| | - Nanwei Tong
- Department of Endocrinology and Metabolism, Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
| | - Guy A. Rutter
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology, and Metabolism, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, United Kingdom
- Le Centre de recherche du Centre hospitalier de l’Université de Montréal (CR-CHUM), University of Montréal, Montréal, QC H2X 0A9, Canada
| | - Markus R. Wenk
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, S117456, Singapore
| | - David L. Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke–National University of Singapore Graduate Medical School, S169857, Singapore
| | - Per-Olof Berggren
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- Singapore Eye Research Institute, Singapore General Hospital, S168751, Singapore
- Department of Endocrinology and Metabolism, Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu 610041, People’s Republic of China
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, S308232, Singapore
- Singapore Eye Research Institute, Singapore General Hospital, S168751, Singapore
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18
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Wong BH, Mei D, Chua GL, Galam DL, Wenk MR, Torta F, Silver DL. The lipid transporter Mfsd2a maintains pulmonary surfactant homeostasis. J Biol Chem 2022; 298:101709. [PMID: 35150739 PMCID: PMC8914330 DOI: 10.1016/j.jbc.2022.101709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
Pulmonary surfactant is a lipoprotein complex essential for lung function, and insufficiency or altered surfactant composition is associated with major lung diseases, such as acute respiratory distress syndromes, idiopathic pulmonary fibrosis, and chronic obstructive pulmonary disease. Pulmonary surfactant is primarily composed of phosphatidylcholine (PC) in complex with specialized surfactant proteins and secreted by alveolar type 2 (AT2) cells. Surfactant homeostasis on the alveolar surface is balanced by the rates of synthesis and secretion with reuptake and recycling by AT2 cells, with some degradation by pulmonary macrophages and loss up the bronchial tree. However, whether phospholipid (PL) transporters exist in AT2 cells to mediate reuptake of surfactant PL remains to be identified. Here, we demonstrate that major facilitator superfamily domain containing 2a (Mfsd2a), a sodium-dependent lysophosphatidylcholine (LPC) transporter, is expressed at the apical surface of AT2 cells. A mouse model with inducible AT2 cell–specific deficiency of Mfsd2a exhibited AT2 cell hypertrophy with reduced total surfactant PL levels because of reductions in the most abundant surfactants, PC containing dipalmitic acid, and PC species containing the omega-3 fatty acid docosahexaenoic acid. These changes in surfactant levels and composition were mirrored by similar changes in the AT2 cell lipidome. Mechanistically, direct tracheal instillation of fluorescent LPC and PC probes indicated that Mfsd2a mediates the uptake of LPC generated by pulmonary phospholipase activity in the alveolar space. These studies reveal that Mfsd2a-mediated LPC uptake is quantitatively important in maintaining surfactant homeostasis and identify this lipid transporter as a physiological component of surfactant recycling.
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Affiliation(s)
- Bernice H Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Ding Mei
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Geok Lin Chua
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Dwight L Galam
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David L Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
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19
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Tan SH, Koh HWL, Chua JY, Burla B, Ong CC, Teo LSL, Yang X, Benke PI, Choi H, Torta F, Richards AM, Wenk MR, Chan MY. Variability of the Plasma Lipidome and Subclinical Coronary Atherosclerosis. Arterioscler Thromb Vasc Biol 2021; 42:100-112. [PMID: 34809445 PMCID: PMC8691371 DOI: 10.1161/atvbaha.121.316847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Supplemental Digital Content is available in the text. Objective: While the risk of acute coronary events has been associated with biological variability of circulating cholesterol, the association with variability of other atherogenic lipids remains less understood. We evaluated the longitudinal variability of 284 lipids and investigated their association with asymptomatic coronary atherosclerosis. Approach and Results: Circulating lipids were extracted from fasting blood samples of 83 community-sampled symptom-free participants (age 41–75 years), collected longitudinally over 6 months. Three types of coronary plaque volume (calcified, lipid-rich, and fibrotic) were quantified using computed tomography coronary angiogram. We first deconvoluted between-subject (CVg) and within-subject (CVw) lipid variabilities. We then tested whether the mean lipid abundance was different across groups categorized by Framingham risk score and plaques phenotypes (lipid-rich, fibrotic, and calcified). Finally, we investigated whether visit-to-visit variability of each lipid was associated with plaque burden. Most lipids (72.5%) exhibited higher CVg than CVw. Among the lipids (n=145) with 1.2-fold higher CVg than CVw, 26 species including glycerides and ceramides were significantly associated with Framingham risk score and the 3 plaque phenotypes (false discovery rate <0.05). In an exploratory analysis of person-specific visit-to-visit variability without multiple testing correction, high variability of 3 lysophospholipids (lysophosphatidylethanolamines 16:0, 18:0, and lysophosphatidylcholine O-18:1) was associated with lipid-rich and fibrotic (noncalcified) plaque volume while high variability of diacylglycerol 18:1_20:0, triacylglycerols 52:2, 52:3, and 52:4, ceramide d18:0/20:0, dihexosylceramide d18:1/16:0, and sphingomyelin 36:3 was associated with calcified plaque volume. Conclusions: High person-specific longitudinal variation of specific nonsterol lipids is associated with the burden of subclinical coronary atherosclerosis. Larger studies are needed to confirm these exploratory findings.
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Affiliation(s)
- Sock Hwee Tan
- Cardiovascular Research Institute (S.H.T., H.W.L.K., X.Y., H.C., A.M.R., M.Y.C.), Singapore Lipidomics Incubator (SLING), National University of Singapore.,National University Heart Center, Singapore (S.H.T., J.Y.C., A.M.R., M.Y.C.)
| | - Hiromi W L Koh
- Cardiovascular Research Institute (S.H.T., H.W.L.K., X.Y., H.C., A.M.R., M.Y.C.), Singapore Lipidomics Incubator (SLING), National University of Singapore
| | - Jing Yi Chua
- National University Heart Center, Singapore (S.H.T., J.Y.C., A.M.R., M.Y.C.)
| | - Bo Burla
- Life Sciences Institute (B.B., P.I.B., F.T., M.R.W.), National University of Singapore
| | - Ching Ching Ong
- Department of Diagnostic Imaging, National University Hospital, Singapore (C.C.O., L.S.L.T.)
| | - Li San Lynette Teo
- Department of Diagnostic Imaging, National University Hospital, Singapore (C.C.O., L.S.L.T.)
| | - Xiaoxun Yang
- Cardiovascular Research Institute (S.H.T., H.W.L.K., X.Y., H.C., A.M.R., M.Y.C.), Singapore Lipidomics Incubator (SLING), National University of Singapore
| | - Peter I Benke
- Life Sciences Institute (B.B., P.I.B., F.T., M.R.W.), National University of Singapore
| | - Hyungwon Choi
- Cardiovascular Research Institute (S.H.T., H.W.L.K., X.Y., H.C., A.M.R., M.Y.C.), Singapore Lipidomics Incubator (SLING), National University of Singapore
| | - Federico Torta
- Department of Biochemistry and Precision Medicine Translational Research Programme (F.T., M.R.W.), Singapore Lipidomics Incubator (SLING), National University of Singapore.,Life Sciences Institute (B.B., P.I.B., F.T., M.R.W.), National University of Singapore
| | - A Mark Richards
- Cardiovascular Research Institute (S.H.T., H.W.L.K., X.Y., H.C., A.M.R., M.Y.C.), Singapore Lipidomics Incubator (SLING), National University of Singapore.,National University Heart Center, Singapore (S.H.T., J.Y.C., A.M.R., M.Y.C.).,Christchurch Heart Institute, University of Otago Christchurch, Christchurch Hospital (A.M.R.)
| | - Markus R Wenk
- Department of Biochemistry and Precision Medicine Translational Research Programme (F.T., M.R.W.), Singapore Lipidomics Incubator (SLING), National University of Singapore.,Life Sciences Institute (B.B., P.I.B., F.T., M.R.W.), National University of Singapore
| | - Mark Y Chan
- Cardiovascular Research Institute (S.H.T., H.W.L.K., X.Y., H.C., A.M.R., M.Y.C.), Singapore Lipidomics Incubator (SLING), National University of Singapore.,National University Heart Center, Singapore (S.H.T., J.Y.C., A.M.R., M.Y.C.)
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20
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Liu Y, Castano D, Girolamo F, Trigueros-Motos L, Bae HG, Neo SP, Oh J, Narayanaswamy P, Torta F, Rye KA, Jo DG, Gunaratne J, Jung S, Virgintino D, Singaraja RR. Abca8b promotes myelination via regulation of chondroitin sulfate proteoglycan 4 localization in oligodendrocyte precursor cells in mice. J Lipid Res 2021; 63:100147. [PMID: 34752805 PMCID: PMC8953628 DOI: 10.1016/j.jlr.2021.100147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 01/29/2023] Open
Abstract
The myelin sheath, which is wrapped around axons, is a lipid-enriched structure produced by mature oligodendrocytes. Disruption of the myelin sheath is observed in several neurological diseases, such as multiple sclerosis. A crucial component of myelin is sphingomyelin, levels of which can be increased by ABCA8, a member of the ATP-binding cassette transporter family. ABCA8 is highly expressed in the cerebellum, specifically in oligodendroglia. However, whether ABCA8 plays a role in myelination and mechanisms that would underlie this role remain unknown. Here, we found that the absence of Abca8b, a mouse ortholog of ABCA8, led to decreased numbers of cerebellar oligodendrocyte precursor cells (OPCs) and mature oligodendrocytes in mice. We show that in oligodendrocytes, ABCA8 interacts with chondroitin sulfate proteoglycan 4 (CSPG4), a molecule essential for OPC proliferation, migration, and myelination. In the absence of Abca8b, localization of CSPG4 to the plasma membrane was decreased, contributing to reduced cerebellar CSPG4 expression. Cerebellar CSPG4+ OPCs were also diminished, leading to decreased mature myelinating oligodendrocyte numbers and cerebellar myelination levels in Abca8b−/− mice. In addition, electron microscopy analyses showed that the number of nonmyelinated cerebellar axons was increased, whereas cerebellar myelin thickness (g-ratio), myelin sheath periodicity, and axonal diameter were all decreased, indicative of disordered myelin ultrastructure. In line with disrupted cerebellar myelination, Abca8b−/− mice showed lower cerebellar conduction velocity and disturbed locomotion. In summary, ABCA8 modulates cerebellar myelination, in part through functional regulation of the ABCA8-interacting protein CSPG4. Our findings suggest that ABCA8 disruption may contribute to the pathophysiology of myelin disorders.
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Affiliation(s)
- Yiran Liu
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cardiovascular Research Institute, National University Health System, Singapore
| | - David Castano
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cardiovascular Research Institute, National University Health System, Singapore
| | - Francesco Girolamo
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs, Human Anatomy and Histology Unit, University of Bari School of Medicine, Bari, Italy
| | - Laia Trigueros-Motos
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore
| | - Han-Gyu Bae
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore
| | - Suat Peng Neo
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Jeongah Oh
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore
| | - Pradeep Narayanaswamy
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore
| | - Kerry Anne Rye
- University of New South Wales, School of Medical Sciences, Sydney, Australia
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Korea
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Sangyong Jung
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, Singapore
| | - Daniela Virgintino
- Department of Basic Medical Sciences, Neurosciences, and Sensory Organs, Human Anatomy and Histology Unit, University of Bari School of Medicine, Bari, Italy
| | - Roshni R Singaraja
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cardiovascular Research Institute, National University Health System, Singapore.
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21
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Loo SY, Toh LP, Xie WH, Pathak E, Tan W, Ma S, Lee MY, Shatishwaran S, Yeo JZZ, Yuan J, Ho YY, Peh EKL, Muniandy M, Torta F, Chan J, Tan TJ, Sim Y, Tan V, Tan B, Madhukumar P, Yong WS, Ong KW, Wong CY, Tan PH, Yap YS, Deng LW, Dent R, Foo R, Wenk MR, Lee SC, Ho YS, Lim EH, Tam WL. Fatty acid oxidation is a druggable gateway regulating cellular plasticity for driving metastasis in breast cancer. Sci Adv 2021; 7:eabh2443. [PMID: 34613780 PMCID: PMC8494440 DOI: 10.1126/sciadv.abh2443] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Cell state transitions control the functional behavior of cancer cells. Epithelial-to-mesenchymal transition (EMT) confers cancer stem cell-like properties, enhanced tumorigenicity and drug resistance to tumor cells, while mesenchymal-epithelial transition (MET) reverses these phenotypes. Using high-throughput chemical library screens, retinoids are found to be potent promoters of MET that inhibit tumorigenicity in basal-like breast cancer. Cell state transitions are defined by reprogramming of lipid metabolism. Retinoids bind cognate nuclear receptors, which target lipid metabolism genes, thereby redirecting fatty acids for β-oxidation in the mesenchymal cell state towards lipid storage in the epithelial cell state. Disruptions of key metabolic enzymes mediating this flux inhibit MET. Conversely, perturbations to fatty acid oxidation (FAO) rechannel fatty acid flux and promote a more epithelial cell phenotype, blocking EMT-driven breast cancer metastasis in animal models. FAO impinges on the epigenetic control of EMT through acetyl-CoA-dependent regulation of histone acetylation on EMT genes, thus determining cell states.
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Affiliation(s)
- Ser Yue Loo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - Li Ping Toh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - William Haowei Xie
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - Elina Pathak
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - Wilson Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - Siming Ma
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - May Yin Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - S. Shatishwaran
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - Joanna Zhen Zhen Yeo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Ju Yuan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - Yin Ying Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Singapore 138668, Singapore
| | - Esther Kai Lay Peh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Singapore 138668, Singapore
| | - Magendran Muniandy
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Jack Chan
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Tira J. Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
- Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Yirong Sim
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Veronique Tan
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Benita Tan
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Preetha Madhukumar
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Wei Sean Yong
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Kong Wee Ong
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Chow Yin Wong
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, 20 College Rd., Singapore 169856, Singapore
| | - Yoon Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
- Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Lih-Wen Deng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Rebecca Dent
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Roger Foo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
| | - Markus R. Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, 5 Lower Kent Ridge Road, Singapore 119074, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Singapore 138668, Singapore
| | - Elaine Hsuen Lim
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
- Corresponding author. (E.H.L.); (W.L.T.)
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore 138672, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Corresponding author. (E.H.L.); (W.L.T.)
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22
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George AD, Gay MCL, Selvalatchmanan J, Torta F, Bendt AK, Wenk MR, Murray K, Wlodek ME, Geddes DT. Healthy Breastfeeding Infants Consume Different Quantities of Milk Fat Globule Membrane Lipids. Nutrients 2021; 13:nu13092951. [PMID: 34578827 PMCID: PMC8471100 DOI: 10.3390/nu13092951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 01/13/2023] Open
Abstract
The human milk fat globule membrane (MFGM) contains important lipids for growing infants. Anthropometric measurements, milk samples, and infant milk intake were collected in a cohort of eleven healthy mother–infant dyads during exclusive breastfeeding from birth to six months. One hundred and sixty-six MFGM lipids were analysed using liquid chromatography-mass spectrometry, and the infant intake was calculated. The concentrations and intake were compared and associations between infant intake and growth characteristics explored. The lipid concentrations and infant intake varied widely between mother–infant dyads and between months one and three. The infant intake for many species displayed positive correlations with infant growth, particularly phospholipid species. The high variation in lipid intake is likely an important factor in infant growth, with strong correlations identified between the intake of many MFGM lipids and infant head circumference and weight. This study highlights the need for intake measurements and inclusion in cohort studies to elucidate the role of the human milk lipidome in infant growth and development.
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Affiliation(s)
- Alexandra D. George
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; (M.C.L.G.); (M.E.W.); (D.T.G.)
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- Correspondence:
| | - Melvin C. L. Gay
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; (M.C.L.G.); (M.E.W.); (D.T.G.)
| | - Jayashree Selvalatchmanan
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (J.S.); (F.T.); (M.R.W.)
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore;
| | - Federico Torta
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (J.S.); (F.T.); (M.R.W.)
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore;
| | - Anne K. Bendt
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore;
| | - Markus R. Wenk
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (J.S.); (F.T.); (M.R.W.)
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore;
| | - Kevin Murray
- School of Population and Global Health, The University of Western Australia, Nedlands, WA 6009, Australia;
| | - Mary E. Wlodek
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; (M.C.L.G.); (M.E.W.); (D.T.G.)
- Department of Physiology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Donna T. Geddes
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; (M.C.L.G.); (M.E.W.); (D.T.G.)
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23
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Ambaw YA, Dahl SR, Chen Y, Greibrokk T, Lundanes E, Lazraq I, Shinde S, Selvalatchmanan J, Wenk MR, Sellergren B, Torta F. Tailored Polymer-Based Selective Extraction of Lipid Mediators from Biological Samples. Metabolites 2021; 11:539. [PMID: 34436480 PMCID: PMC8398397 DOI: 10.3390/metabo11080539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
Lipid mediators, small molecules involved in regulating inflammation and its resolution, are a class of lipids of wide interest as their levels in blood and tissues may be used to monitor health and disease states or the effect of new treatments. These molecules are present at low levels in biological samples, and an enrichment step is often needed for their detection. We describe a rapid and selective method that uses new low-cost molecularly imprinted (MIP) and non-imprinted (NIP) polymeric sorbents for the extraction of lipid mediators from plasma and tissue samples. The extraction process was carried out in solid-phase extraction (SPE) cartridges, manually packed with the sorbents. After extraction, lipid mediators were quantified by liquid chromatography-tandem mass spectrometry (LC-MSMS). Various parameters affecting the extraction efficiency were evaluated to achieve optimal recovery and to reduce non-specific interactions. Preliminary tests showed that MIPs, designed using the prostaglandin biosynthetic precursor arachidonic acid, could effectively enrich prostaglandins and structurally related molecules. However, for other lipid mediators, MIP and NIP displayed comparable recoveries. Under optimized conditions, the recoveries of synthetic standards ranged from 62% to 100%. This new extraction method was applied to the determination of the lipid mediators concentration in human plasma and mouse tissues and compared to other methods based on commercially available cartridges. In general, the methods showed comparable performances. In terms of structural specificity, our newly synthesized materials accomplished better retention of prostaglandins (PGs), hydroxydocosahexaenoic acid (HDoHE), HEPE, hydroxyeicosatetraenoic acids (HETE), hydroxyeicosatrienoic acid (HETrE), and polyunsaturated fatty acid (PUFA) compounds, while the commercially available Strata-X showed a higher recovery for dihydroxyeicosatetraenoic acid (diHETrEs). In summary, our results suggest that this new material can be successfully implemented for the extraction of lipid mediators from biological samples.
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Affiliation(s)
- Yohannes Abere Ambaw
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (Y.A.A.); (J.S.); (M.R.W.)
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Harvard University, Cambridge, MA 02138, USA
| | - Sandra Rinne Dahl
- Department of Chemistry, University of Oslo, 0315 Oslo, Norway; (S.R.D.); (Y.C.); (T.G.); (E.L.)
- Hormone Laboratory, Department of Medical Biochemistry, Oslo University Hospital, 0424 Oslo, Norway
| | - Yan Chen
- Department of Chemistry, University of Oslo, 0315 Oslo, Norway; (S.R.D.); (Y.C.); (T.G.); (E.L.)
| | - Tyge Greibrokk
- Department of Chemistry, University of Oslo, 0315 Oslo, Norway; (S.R.D.); (Y.C.); (T.G.); (E.L.)
| | - Elsa Lundanes
- Department of Chemistry, University of Oslo, 0315 Oslo, Norway; (S.R.D.); (Y.C.); (T.G.); (E.L.)
| | - Issam Lazraq
- Department of Biomedical Sciences, Biofilms Research Center for Biointerfaces, Faculty of Health and Society, Malmö University, 21119 Malmö, Sweden; (I.L.); (S.S.)
| | - Sudhirkumar Shinde
- Department of Biomedical Sciences, Biofilms Research Center for Biointerfaces, Faculty of Health and Society, Malmö University, 21119 Malmö, Sweden; (I.L.); (S.S.)
- School of Consciousness, Dr Vishwanath Karad Maharashtra Institute of Technology–World Peace University, Kothrud, Pune 411038, Maharashtra, India
| | - Jayashree Selvalatchmanan
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (Y.A.A.); (J.S.); (M.R.W.)
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
| | - Markus R. Wenk
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (Y.A.A.); (J.S.); (M.R.W.)
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
| | - Börje Sellergren
- Department of Biomedical Sciences, Biofilms Research Center for Biointerfaces, Faculty of Health and Society, Malmö University, 21119 Malmö, Sweden; (I.L.); (S.S.)
| | - Federico Torta
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore; (Y.A.A.); (J.S.); (M.R.W.)
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
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24
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Olona A, Hateley C, Muralidharan S, Wenk MR, Torta F, Behmoaras J. Sphingolipid metabolism during Toll-like receptor 4 (TLR4)-mediated macrophage activation. Br J Pharmacol 2021; 178:4575-4587. [PMID: 34363204 DOI: 10.1111/bph.15642] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/18/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
Macrophage activation in response to stimulation of Toll-like receptor 4 (TLR4) provides a paradigm for investigating energy metabolism that regulates the inflammatory response. TLR4-mediated pro-inflammatory macrophage activation is characterized by increased glycolysis and altered mitochondrial metabolism, supported by selective amino acid uptake and/or usage. Fatty acid metabolism remains as a highly complex rewiring that accompanies classical macrophage activation. TLR4 activation leads to de novo synthesis of fatty acids, which flux into sphingolipids, complex lipids that form the building blocks of eukaryotic cell membranes and regulate cell function. Here, we review the importance of TLR4-mediated de novo synthesis of membrane sphingolipids in macrophages. We first highlight fatty acid metabolism during TLR4-driven macrophage immunometabolism. We then focus on the temporal dynamics of sphingolipid biosynthesis and emphasize the modulatory role of some sphingolipid species (i.e. sphingomyelins, ceramides and glycosphingolipids) on the pro-inflammatory and pro-resolution phases of LPS/TLR4 activation in macrophages.
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Affiliation(s)
- Antoni Olona
- Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK
| | - Charlotte Hateley
- Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK
| | | | - Markus R Wenk
- SLING, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Federico Torta
- SLING, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jacques Behmoaras
- Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK.,Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School Singapore, Republic of Singapore
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25
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Ren H, Triebl A, Muralidharan S, Wenk MR, Xia Y, Torta F. Mapping the distribution of double bond location isomers in lipids across mouse tissues. Analyst 2021; 146:3899-3907. [PMID: 34009216 DOI: 10.1039/d1an00449b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lipids are highly diverse and essential biomolecules in all living systems. As lipid homeostasis is often perturbed in metabolic diseases, these molecules can serve as both biomarkers and drug targets. The development of modern mass spectrometry (MS) provided the platform for large-scale lipidomic studies at the level of molecular species. Traditionally, more detailed structural information, such as the C[double bond, length as m-dash]C location, was mostly assumed instead of properly measured, though the specific isomers were indicated as potential biomarkers of cancers or cardiovascular diseases. Recent C[double bond, length as m-dash]C localization methods, including the Paternò-Büchi (PB) reaction, have shown the prevalent and heterogeneous distribution of C[double bond, length as m-dash]C location in lipids across tissues. Mapping the lipidome of model animals at the level of C[double bond, length as m-dash]C position would increase the understanding of the metabolism and function of lipid isomers, facilitating clinical research. In this study, we employed an online PB reaction on a liquid chromatography-high resolution MS platform to map C[double bond, length as m-dash]C location isomers in five different murine tissues. We analyzed phosphatidylcholines, phosphatidylethanolamines, and sphingomyelins; we relatively quantified and mapped the distribution of ∼30 groups of co-existing isomers, characterized by different chain lengths and degrees of unsaturation. More specifically, we performed relative quantitation of four isomers of the C16:1 fatty acyl, which included rarely reported n-10 and n-5 species besides n-9 and n-7 isomers. We showed a small variation of the isomers' relative composition among individual animals (<20%) but significant differences across different lipid species and mouse tissues. Our results provided an initial database to map alternative lipid metabolic pathways at the tissue level.
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Affiliation(s)
- Hanlin Ren
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Alexander Triebl
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore. and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sneha Muralidharan
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore.
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore. and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore. and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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26
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Muralidharan S, Shimobayashi M, Ji S, Burla B, Hall MN, Wenk MR, Torta F. A reference map of sphingolipids in murine tissues. Cell Rep 2021; 35:109250. [PMID: 34133933 DOI: 10.1016/j.celrep.2021.109250] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/21/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Sphingolipids (SPs) have both a structural role in the cell membranes and a signaling function that regulates many cellular processes. The enormous structural diversity and low abundance of many SPs pose a challenge for their identification and quantification. Recent advances in lipidomics, in particular liquid chromatography (LC) coupled with mass spectrometry (MS), provide methods to detect and quantify many low-abundant SP species reliably. Here we use LC-MS to compile a "murine sphingolipid atlas," containing the qualitative and quantitative distribution of 114 SPs in 21 tissues of a widely utilized wild-type laboratory mouse strain (C57BL/6). We report tissue-specific SP fingerprints, as well as sex-specific differences in the same tissue. This is a comprehensive, quantitative sphingolipidomic map of mammalian tissues collected in a systematic fashion. It will complement other tissue compendia for interrogation into the role of SP in mammalian health and disease.
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Affiliation(s)
- Sneha Muralidharan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Mitsugu Shimobayashi
- Biozentrum - Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Shanshan Ji
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Michael N Hall
- Biozentrum - Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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27
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Hoong JSY, Chew WS, Torta F, Khoo CM, Wenk MR, Herr DR, Tai ES, van Dam RM. Dietary Fat and Protein Intakes in Relation to Plasma Sphingolipids As Determined by a Large-Scale Lipidomic Analysis. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab047_024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Objectives
Sphingolipid concentrations have been associated with risk of type 2 diabetes and cardiovascular diseases. Because sphingolipids can be synthesized de novo from saturated fatty acids (SFA), dietary fatty acids may affect plasma sphingolipid concentrations. We aimed to evaluate dietary fat and protein intakes in relation to circulating sphingolipid levels.
Methods
We used cross-sectional data from 2860 ethnic Chinese Singaporeans collected from 2004–2007. Nutrient intakes were estimated on the basis of a validated 159-item food frequency questionnaire. We quantified 79 molecularly distinct sphingolipids in a large-scale lipidomic evaluation from plasma samples.
Results
Higher saturated fat intake was associated with higher concentrations of 16:1; O2 sphingolipids including ceramides, monohexosylcermides, dihexosylceramides, sphingomyelins, and sphingosine 1-phosphates. Higher polyunsaturated fat intake was associated with lower plasma long-chain ceramides and long-chain monohexosylcermide concentrations. Protein intake was inversely associated with concentrations of most subclasses of sphingolipids, with the exception of sphingolipids containing a 16:1; O2 sphingoid base. Lower intake of saturated fat and higher intake of polyunsaturated fat and protein may decrease plasma concentrations of several sphingolipid classes.
Conclusions
These findings may represent a novel biological mechanism for the impact of nutrient intakes on cardio-metabolic health.
Funding Sources
This work was supported by the National Research Foundation Investigatorship grant (NRF-NRFI2015–05, to MRW), A*STAR (I1901E0040), and the National University Health System (NUHSRO/2014/085/AF-Partner/01, DRH). FT was supported by the NRF and A*STAR IAF-ICP I1901E0040.
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28
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Alsanafi M, Brown RDR, Oh J, Adams DR, Torta F, Pyne NJ, Pyne S. Dihydroceramide Desaturase Functions as an Inducer and Rectifier of Apoptosis: Effect of Retinol Derivatives, Antioxidants and Phenolic Compounds. Cell Biochem Biophys 2021; 79:461-475. [PMID: 33991313 PMCID: PMC8551130 DOI: 10.1007/s12013-021-00990-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/24/2021] [Indexed: 11/24/2022]
Abstract
Dihydroceramide desaturase (Degs1) catalyses the introduction of a 4,5-trans double bond into dihydroceramide to form ceramide. We show here that Degs1 is polyubiquitinated in response to retinol derivatives, phenolic compounds or anti-oxidants in HEK293T cells. The functional predominance of native versus polyubiquitinated forms of Degs1 appears to govern cytotoxicity. Therefore, 4-HPR or celecoxib appear to stimulate the de novo ceramide pathway (with the exception of C24:0 ceramide), using native Degs1, and thereby promote PARP cleavage and LC3B-I/II processing (autophagy/apoptosis). The ubiquitin-proteasomal degradation of Degs1 is positively linked to cell survival via XBP-1s and results in a concomitant increase in dihydroceramides and a decrease in C24:0 ceramide levels. However, in the case of 4-HPR or celecoxib, the native form of Degs1 functionally predominates, such that the apoptotic programme is sustained. In contrast, 4-HPA or AM404 do not produce apoptotic ceramide, using native Degs1, but do promote a rectifier function to induce ubiquitin-proteasomal degradation of Degs1 and are not cytotoxic. Therefore, Degs1 appears to function both as an ‘inducer’ and ‘rectifier’ of apoptosis in response to chemical cellular stress, the dynamic balance for which is dependent on the nature of chemical stress, thereby determining cytotoxicity. The de novo synthesis of ceramide or the ubiquitin-proteasomal degradation of Degs1 in response to anti-oxidants, retinol derivatives and phenolic compounds appear to involve sensors, and for rectifier function, this might be Degs1 itself.
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Affiliation(s)
- Mariam Alsanafi
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Ryan D R Brown
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Jeongah Oh
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute and Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - David R Adams
- School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Federico Torta
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute and Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nigel J Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Susan Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK.
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29
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Brown RDR, Veerman BEP, Oh J, Tate RJ, Torta F, Cunningham MR, Adams DR, Pyne S, Pyne NJ. A new model for regulation of sphingosine kinase 1 translocation to the plasma membrane in breast cancer cells. J Biol Chem 2021; 296:100674. [PMID: 33865856 PMCID: PMC8135045 DOI: 10.1016/j.jbc.2021.100674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/01/2021] [Accepted: 04/14/2021] [Indexed: 01/24/2023] Open
Abstract
The translocation of sphingosine kinase 1 (SK1) to the plasma membrane (PM) is crucial in promoting oncogenesis. We have previously proposed that SK1 exists as both a monomer and dimer in equilibrium, although it is unclear whether these species translocate to the PM via the same or different mechanisms. We therefore investigated the structural determinants involved to better understand how translocation might potentially be targeted for therapeutic intervention. We report here that monomeric WT mouse SK1 (GFP-mSK1) translocates to the PM of MCF-7L cells stimulated with carbachol or phorbol 12-myristate 13-acetate, whereas the dimer translocates to the PM in response to sphingosine-1-phosphate; thus, the equilibrium between the monomer and dimer is sensitive to cellular stimulus. In addition, carbachol and phorbol 12-myristate 13-acetate induced translocation of monomeric GFP-mSK1 to lamellipodia, whereas sphingosine-1-phosphate induced translocation of dimeric GFP-mSK1 to filopodia, suggesting that SK1 regulates different cell biological processes dependent on dimerization. GFP-mSK1 mutants designed to modulate dimerization confirmed this difference in localization. Regulation by the C-terminal tail of SK1 was investigated using GFP-mSK1 truncations. Removal of the last five amino acids (PPEEP) prevented translocation of the enzyme to the PM, whereas removal of the last ten amino acids restored translocation. This suggests that the penultimate five amino acids (SRRGP) function as a translocation brake, which can be released by sequestration of the PPEEP sequence. We propose that these determinants alter the arrangement of N-terminal and C-terminal domains in SK1, leading to unique surfaces that promote differential translocation to the PM.
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Affiliation(s)
- Ryan D R Brown
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Ben E P Veerman
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Jeongah Oh
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute and Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rothwelle J Tate
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Federico Torta
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute and Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Margaret R Cunningham
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - David R Adams
- School of Engineering & Physical Sciences, Heriot-Watt University, Edinburgh, UK
| | - Susan Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Nigel J Pyne
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK.
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30
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Chandrakanthan M, Nguyen TQ, Hasan Z, Muralidharan S, Vu TM, Li AWL, Le UTN, Thi Thuy Ha H, Baik SH, Tan SH, Foo JC, Wenk MR, Cazenave-Gassiot A, Torta F, Ong WY, Chan MYY, Nguyen LN. Deletion of Mfsd2b impairs thrombotic functions of platelets. Nat Commun 2021; 12:2286. [PMID: 33863882 PMCID: PMC8052357 DOI: 10.1038/s41467-021-22642-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/23/2021] [Indexed: 11/09/2022] Open
Abstract
We recently discovered that Mfsd2b, which is the S1P exporter found in blood cells. Here, we report that Mfsd2b is critical for the release of all S1P species in both resting and activated platelets. We show that resting platelets store S1P in the cytoplasm. After activation, this S1P pool is delivered to the plasma membrane, where Mfsd2b is predominantly localized for export. Employing knockout mice of Mfsd2b, we reveal that platelets contribute a minor amount of plasma S1P. Nevertheless, Mfsd2b deletion in whole body or platelets impairs platelet morphology and functions. In particular, Mfsd2b knockout mice show significantly reduced thrombus formation. We show that loss of Mfsd2b affects intrinsic platelet functions as part of remarkable sphingolipid accumulation. These findings indicate that accumulation of sphingolipids including S1P by deletion of Mfsd2b strongly impairs platelet functions, which suggests that the transporter may be a target for the prevention of thrombotic disorders.
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Affiliation(s)
- Madhuvanthi Chandrakanthan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Toan Quoc Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zafrul Hasan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sneha Muralidharan
- Department of Medicine, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Thiet Minh Vu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Aaron Wei Liang Li
- Department of Medicine, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Uyen Thanh Nha Le
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hoa Thi Thuy Ha
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sang-Ha Baik
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sock Hwee Tan
- Department of Medicine, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Juat Chin Foo
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Wei Yi Ong
- Department of Anatomy, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mark Yan Yee Chan
- Department of Medicine, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Long N Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore. .,Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Immunology Program Research Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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31
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Seah JYH, Chew WS, Torta F, Khoo CM, Wenk MR, Herr DR, Tai ES, van Dam RM. Dietary Fat and Protein Intake in Relation to Plasma Sphingolipids as Determined by a Large-Scale Lipidomic Analysis. Metabolites 2021; 11:metabo11020093. [PMID: 33567768 PMCID: PMC7915172 DOI: 10.3390/metabo11020093] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/24/2022] Open
Abstract
Sphingolipid concentrations have been associated with risk of type 2 diabetes and cardiovascular diseases. Because sphingolipids can be synthesized de novo from saturated fatty acids (SFA), dietary fatty acids may affect plasma sphingolipid concentrations. We aimed to evaluate dietary fat and protein intakes in relation to circulating sphingolipid levels. We used cross-sectional data from 2860 ethnic Chinese Singaporeans collected from 2004–2007. Nutrient intakes were estimated on the basis of a validated 159-item food frequency questionnaire. We quantified 79 molecularly distinct sphingolipids in a large-scale lipidomic evaluation from plasma samples. Higher saturated fat intake was associated with higher concentrations of 16:1;O2 sphingolipids including ceramides, monohexosylcermides, dihexosylceramides, sphingomyelins, and sphingosine 1-phosphates. Higher polyunsaturated fat intake was associated with lower plasma long-chain ceramides and long-chain monohexosylcermide concentrations. Protein intake was inversely associated with concentrations of most subclasses of sphingolipids, with the exception of sphingolipids containing a 16:1;O2 sphingoid base. Lower intake of saturated fat and higher intake of polyunsaturated fat and protein may decrease plasma concentrations of several sphingolipid classes. These findings may represent a novel biological mechanism for the impact of nutrient intakes on cardio-metabolic health.
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Affiliation(s)
- Jowy Yi Hoong Seah
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), Singapore 117549, Singapore;
- NUS Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077, Singapore
- Correspondence: (J.Y.H.S.); (R.M.v.D.); Tel.: +65-6516-4980 (R.M.v.D.)
| | - Wee Siong Chew
- Department of Pharmacology, Yong Loo Lin School of Medicine, NUS, Singapore 117600, Singapore; (W.S.C.); (D.R.H.)
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore 117596, Singapore; (F.T.); (M.R.W.)
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore 117456, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, NUS and National University Health System, Singapore 119228, Singapore;
| | - Markus R. Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore 117596, Singapore; (F.T.); (M.R.W.)
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore 117456, Singapore
| | - Deron R. Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, NUS, Singapore 117600, Singapore; (W.S.C.); (D.R.H.)
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), Singapore 117549, Singapore;
- Department of Medicine, Yong Loo Lin School of Medicine, NUS and National University Health System, Singapore 119228, Singapore;
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Rob M. van Dam
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), Singapore 117549, Singapore;
- NUS Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077, Singapore
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Correspondence: (J.Y.H.S.); (R.M.v.D.); Tel.: +65-6516-4980 (R.M.v.D.)
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32
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Gao L, Ji S, Burla B, Wenk MR, Torta F, Cazenave-Gassiot A. LICAR: An Application for Isotopic Correction of Targeted Lipidomic Data Acquired with Class-Based Chromatographic Separations Using Multiple Reaction Monitoring. Anal Chem 2021; 93:3163-3171. [PMID: 33535740 DOI: 10.1021/acs.analchem.0c04565] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lipidomics is developing as an important area in biomedical and clinical research. Reliable quantification of lipid species is required for clinical translation of lipidomic studies. Hydrophilic interaction chromatography (HILIC), normal-phase liquid chromatography (NPLC), and supercritical fluid chromatography (SFC) are commonly used techniques in lipidomics and provide class-based separation of lipids. While co-elution of lipid species and their internal standards is an advantage for accurate quantification, it leads to isotopic overlap between species of the same lipid class. In shotgun lipidomics, isotopic correction is typically done based on elemental formulas of precursor ions. In multiple reaction monitoring (MRM) analyses, however, this approach should not be used, as the overall contribution of heavy isotopes to the MRM transitions' intensities depends on their location in the molecule with respect to the fragmentation pattern. We present an algorithm, provided in the R programming language, for isotopic correction in class-based separation using MRM, extracting relevant structural information from MRM transitions to apply adequate isotopic correction factors. Using standards, we show that our algorithm accurately estimates the isotopic contribution of isotopologues to MRM transitions' measured intensities. Using human plasma as an example, we demonstrate the necessity of adequate isotopic correction for accurate quantitation of lipids measured by MRM with class-based chromatographic separation. We show that over a third of the measured phosphatidylcholine species had their intensity corrected by more than 10%. This isotopic correction algorithm and R-implemented application enable a more accurate quantification of lipids in class-based separation-MRM, a prerequisite for successful translation of lipidomic applications.
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Affiliation(s)
- Liang Gao
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore.,Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore
| | - Shanshan Ji
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore.,Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore.,Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore.,Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, 28 Medical Drive #03-03, 117456 Singapore
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33
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Nguyen TQ, Vu TM, Tukijan F, Muralidharan S, Foo JC, Li Chin JF, Hasan Z, Torta F, Nguyen LN. Erythrocytes efficiently utilize exogenous sphingosines for S1P synthesis and export via Mfsd2b. J Biol Chem 2020; 296:100201. [PMID: 33334894 PMCID: PMC7948482 DOI: 10.1074/jbc.ra120.012941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 11/24/2020] [Accepted: 12/16/2020] [Indexed: 12/29/2022] Open
Abstract
Sphingosine-1-phosphate (S1P) is a potent lipid mediator that exerts its activity via activation of five different G protein–coupled receptors, designated as S1P1–5. This potent lipid mediator is synthesized from the sphingosine precursor by two sphingosine kinases (SphK1 and 2) and must be exported to exert extracellular signaling functions. We recently identified Mfsd2b as the S1P transporter in the hematopoietic system. However, the sources of sphingosine for S1P synthesis and the transport mechanism of Mfsd2b in erythrocytes remain to be determined. Here, we show that erythrocytes efficiently take up exogenous sphingosine and that a de novo synthesis pathway in part provides sphingosines to erythrocytes. The uptake of sphingosine in erythrocytes is facilitated by the activity of SphK1. By converting sphingosine into S1P, SphK1 indirectly increases the influx of sphingosine, a process that is irreversible in erythrocytes. Our results explain for the abnormally high amount of sphingosine accumulation in Mfsd2b knockout erythrocytes. Furthermore, we show that Mfsd2b utilizes a proton gradient to facilitate the release of S1P. The negatively charged residues D95 and T157 are essential for Mfsd2b transport activity. Of interest, we also discovered an S1P analog that inhibits S1P export from erythrocytes, providing evidence that sphingosine analogs can be used to inhibit S1P export by Mfsd2b. Collectively, our results highlight that erythrocytes are efficient in sphingosine uptake for S1P production and the release of S1P is dependent on Mfsd2b functions.
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Affiliation(s)
- Toan Q Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Thiet Minh Vu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Farhana Tukijan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sneha Muralidharan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Juat Chin Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Zafrul Hasan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Long N Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; SLING/Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; Immunology Translational and Cardiovascular Disease Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Kutuzova S, Colaianni P, Röst H, Sachsenberg T, Alka O, Kohlbacher O, Burla B, Torta F, Schrübbers L, Kristensen M, Nielsen L, Herrgård MJ, McCloskey D. SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing. Anal Chem 2020; 92:15968-15974. [PMID: 33269929 DOI: 10.1021/acs.analchem.0c03421] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Technological advances in high-resolution mass spectrometry (MS) vastly increased the number of samples that can be processed in a life science experiment, as well as volume and complexity of the generated data. To address the bottleneck of high-throughput data processing, we present SmartPeak (https://github.com/AutoFlowResearch/SmartPeak), an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of capillary electrophoresis-, gas chromatography-, and liquid chromatography (LC)-MS(/MS) data and high-pressure LC data for targeted and semitargeted metabolomics, lipidomics, and fluxomics experiments. The application allows for an approximate 100-fold reduction in the data processing time compared to manual processing while enhancing quality and reproducibility of the results.
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Affiliation(s)
- Svetlana Kutuzova
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Pasquale Colaianni
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Hannes Röst
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto M5S 1A8, Canada.,Department of Computer Science, University of Toronto, 40 St. George Street, Toronto M5T 3A1, Canada
| | - Timo Sachsenberg
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Geschwister-Scholl-Platz, Tübingen 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72074, Germany
| | - Oliver Alka
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Geschwister-Scholl-Platz, Tübingen 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72074, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Geschwister-Scholl-Platz, Tübingen 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72074, Germany.,Biomolecular Interactions, MPI for Developmental Biology, Tübingen 72076, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen 72076, Germany
| | - Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 117456, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 117597, Singapore
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Mette Kristensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Lars Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark.,BioInnovation Institute, Ole Maaløes Vej 3, Copenhagen N 2830, Denmark
| | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Lyngby 2800, Denmark
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35
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Ambaw YA, Fuchs D, Raida M, Mazengia NT, Torta F, Wheelock CE, Wenk MR, Tong L. Changes of tear lipid mediators after eyelid warming or thermopulsation treatment for meibomian gland dysfunction. Prostaglandins Other Lipid Mediat 2020; 151:106474. [DOI: 10.1016/j.prostaglandins.2020.106474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/26/2020] [Accepted: 07/14/2020] [Indexed: 01/17/2023]
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36
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Benke PI, Burla B, Ekroos K, Wenk MR, Torta F. Impact of ion suppression by sample cap liners in lipidomics. Anal Chim Acta 2020; 1137:136-142. [PMID: 33153597 DOI: 10.1016/j.aca.2020.09.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/14/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022]
Abstract
Contamination from the polymeric material released by vial caps used for sample introduction in liquid chromatography can significantly affect the signal of the analyte of interest. In particular, repeated injections from the same sample vial can enhance this suppressing effect. Multiple injections of the same sample are often used in metabolomics and lipidomics during routine analyses. Here we demonstrate how the presence of contaminant polymers, originating from the vial closures, significantly influences the estimation of the relative amount of endogenous lipids in human plasma. Furthermore, this can negatively impact other operations in mass spectrometric analysis, such as instrument equilibration and tuning or the common use of technical replicates to improve confidence in data interpretation. Our observations provide critical information on how to improve future analyses through the use of appropriate vial caps, solvents, chromatographic separations and equipment.
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Affiliation(s)
- Peter I Benke
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Kim Ekroos
- Lipidomics Consulting Ltd, Irisviksvägen 31D, 02230, Esbo, Finland
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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37
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Seow WJ, Low DY, Pan WC, Gunther SH, Sim X, Torta F, Herr DR, Kovalik JP, Ching J, Khoo CM, Wenk MR, Tai ES, van Dam RM. Coffee, Black Tea, and Green Tea Consumption in Relation to Plasma Metabolites in an Asian Population. Mol Nutr Food Res 2020; 64:e2000527. [PMID: 33120436 DOI: 10.1002/mnfr.202000527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/06/2020] [Indexed: 12/14/2022]
Abstract
SCOPE Coffee and tea are among the most popular beverages in the world. However, the association between habitual coffee, green tea, and black tea consumption with metabolomics profiles in Asian populations remain largely unknown. METHODS AND RESULTS 158 metabolites (14 amino acids, 45 acylcarnitines, and 99 sphingolipids) in the blood plasma of participants are measured from the population-based Singapore Prospective Study Program cohort using mass spectrometry (MS). Linear regression models are used to obtain the estimates for the association between coffee and tea consumption with metabolite levels, adjusted for potential confounders and false discovery rate (FDR). Coffee consumption is significantly associated with higher levels of 63 sphingolipids (29 sphingomyelins, 32 ceramides, a sphingosine-1-phosphate, and a sphingosine) and lower levels of 13 acylcarnitines and alanine. Black tea consumption is significantly associated with higher levels of eight sphingolipids, and lower levels of an amino acid, whereas green tea is significantly inversely associated with four metabolites (C8:1-OH acylcarnitine, ganglioside GM3 d18:1/16:0, sphingomyelins d18:2/18:0 and d18:1/14:0). CONCLUSIONS Coffee, black tea, and green tea consumption are associated with plasma levels of certain classes of sphingolipids and acylcarnitines in an Asian population, particularly sphingomyelins, which may mediate the health benefits of these beverages.
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Affiliation(s)
- Wei Jie Seow
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, 119228, Singapore
| | - Dorrain Yanwen Low
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Wen-Chi Pan
- Institute of Environmental and Occupational Health Science, School of Medicine, National Yang-Ming University, Taipei, 11221, Taiwan
| | - Samuel H Gunther
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, 119228, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Deron R Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Jean-Paul Kovalik
- Cardiovascular and Metabolic Disorders Programme, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Jianhong Ching
- Cardiovascular and Metabolic Disorders Programme, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, 119228, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, 119228, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, 119228, Singapore
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38
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Chai JF, Raichur S, Khor IW, Torta F, Chew WS, Herr DR, Ching J, Kovalik JP, Khoo CM, Wenk MR, Tai ES, Sim X. Associations with metabolites in Chinese suggest new metabolic roles in Alzheimer's and Parkinson's diseases. Hum Mol Genet 2020; 29:189-201. [PMID: 31628463 DOI: 10.1093/hmg/ddz246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/19/2019] [Accepted: 10/08/2019] [Indexed: 11/14/2022] Open
Abstract
Metabolites are small intermediate products of cellular metabolism perturbed in a variety of complex disorders. Identifying genetic markers associated with metabolite concentrations could delineate disease-related metabolic pathways in humans. We tested genetic variants for associations with 136 metabolites in 1954 Chinese from Singapore. At a conservative genome-wide threshold (3.7 × 10-10), we detected 1899 variant-metabolite associations at 16 genetic loci. Three loci (ABCA7, A4GALT, GSTM2) represented novel associations with metabolites, with the strongest association observed between ABCA7 and d18:1/24:1 dihexosylceramide. Among 13 replicated loci, we identified six new variants independent of previously reported metabolite or lipid signals. We observed variant-metabolite associations at two loci (ABCA7, CHCHD2) that have been linked to neurodegenerative diseases. At SGPP1 and SPTLC3 loci, genetic variants showed preferential selectivity for sphingolipids with d16 (rather than d18) sphingosine backbone, including sphingosine-1-phosphate (S1P). Our results provide new genetic associations for metabolites and highlight the role of metabolites as intermediate modulators in disease metabolic pathways.
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Affiliation(s)
- Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | | | - Ing Wei Khor
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee Siong Chew
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Deron Raymond Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianhong Ching
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Jean-Paul Kovalik
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
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39
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Evans AM, O'Donovan C, Playdon M, Beecher C, Beger RD, Bowden JA, Broadhurst D, Clish CB, Dasari S, Dunn WB, Griffin JL, Hartung T, Hsu PC, Huan T, Jans J, Jones CM, Kachman M, Kleensang A, Lewis MR, Monge ME, Mosley JD, Taylor E, Tayyari F, Theodoridis G, Torta F, Ubhi BK, Vuckovic D. Dissemination and analysis of the quality assurance (QA) and quality control (QC) practices of LC-MS based untargeted metabolomics practitioners. Metabolomics 2020; 16:113. [PMID: 33044703 PMCID: PMC7641040 DOI: 10.1007/s11306-020-01728-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/20/2020] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The metabolomics quality assurance and quality control consortium (mQACC) evolved from the recognized need for a community-wide consensus on improving and systematizing quality assurance (QA) and quality control (QC) practices for untargeted metabolomics. OBJECTIVES In this work, we sought to identify and share the common and divergent QA and QC practices amongst mQACC members and collaborators who use liquid chromatography-mass spectrometry (LC-MS) in untargeted metabolomics. METHODS All authors voluntarily participated in this collaborative research project by providing the details of and insights into the QA and QC practices used in their laboratories. This sharing was enabled via a six-page questionnaire composed of over 120 questions and comment fields which was developed as part of this work and has proved the basis for ongoing mQACC outreach. RESULTS For QA, many laboratories reported documenting maintenance, calibration and tuning (82%); having established data storage and archival processes (71%); depositing data in public repositories (55%); having standard operating procedures (SOPs) in place for all laboratory processes (68%) and training staff on laboratory processes (55%). For QC, universal practices included using system suitability procedures (100%) and using a robust system of identification (Metabolomics Standards Initiative level 1 identification standards) for at least some of the detected compounds. Most laboratories used QC samples (>86%); used internal standards (91%); used a designated analytical acquisition template with randomized experimental samples (91%); and manually reviewed peak integration following data acquisition (86%). A minority of laboratories included technical replicates of experimental samples in their workflows (36%). CONCLUSIONS Although the 23 contributors were researchers with diverse and international backgrounds from academia, industry and government, they are not necessarily representative of the worldwide pool of practitioners due to the recruitment method for participants and its voluntary nature. However, both questionnaire and the findings presented here have already informed and led other data gathering efforts by mQACC at conferences and other outreach activities and will continue to evolve in order to guide discussions for recommendations of best practices within the community and to establish internationally agreed upon reporting standards. We very much welcome further feedback from readers of this article.
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Affiliation(s)
| | - Claire O'Donovan
- European Molecular Biology Laboratory (EMBL), The European Bioinformatics Institute, Cambridgeshire, UK
| | | | | | - Richard D Beger
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - John A Bowden
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - David Broadhurst
- Centre for Integrative Metabolomics & Computational Biology, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | | | - Surendra Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Warwick B Dunn
- School of Biosciences, Phenome Centre Birmingham and Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Julian L Griffin
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Thomas Hartung
- Center for Alternatives To Animal Testing (CAAT), Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ping- Ching Hsu
- University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Judith Jans
- University Medical Center Utrecht, Utrecht, Netherlands
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Andre Kleensang
- Center for Alternatives To Animal Testing (CAAT), Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew R Lewis
- National Phenome Centre, Imperial College London, London, UK
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), C1425FQD, Ciudad de Buenos Aires, Argentina
| | - Jonathan D Mosley
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Washington, DC, USA
| | | | - Fariba Tayyari
- Department of Internal Medicine, Metabolomics Core, The University of Iowa, Iowa City, Iowa, USA
| | | | - Federico Torta
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore
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40
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Tran TM, Ma Z, Triebl A, Nath S, Cheng Y, Gong BQ, Han X, Wang J, Li JF, Wenk MR, Torta F, Mayor S, Yang L, Miao Y. The bacterial quorum sensing signal DSF hijacks Arabidopsis thaliana sterol biosynthesis to suppress plant innate immunity. Life Sci Alliance 2020; 3:e202000720. [PMID: 32788227 PMCID: PMC7425213 DOI: 10.26508/lsa.202000720] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/26/2020] [Accepted: 07/30/2020] [Indexed: 01/04/2023] Open
Abstract
Quorum sensing (QS) is a recognized phenomenon that is crucial for regulating population-related behaviors in bacteria. However, the direct specific effect of QS molecules on host biology is largely understudied. In this work, we show that the QS molecule DSF (cis-11-methyl-dodecenoic acid) produced by Xanthomonas campestris pv. campestris can suppress pathogen-associated molecular pattern-triggered immunity (PTI) in Arabidopsis thaliana, mediated by flagellin-induced activation of flagellin receptor FLS2. The DSF-mediated attenuation of innate immunity results from the alteration of FLS2 nanoclusters and endocytic internalization of plasma membrane FLS2. DSF altered the lipid profile of Arabidopsis, with a particular increase in the phytosterol species, which impairs the general endocytosis pathway mediated by clathrin and FLS2 nano-clustering on the plasma membrane. The DSF effect on receptor dynamics and host immune responses could be entirely reversed by sterol removal. Together, our results highlighted the importance of sterol homeostasis to plasma membrane organization and demonstrate a novel mechanism by which pathogenic bacteria use their communicating molecule to manipulate pathogen-associated molecular pattern-triggered host immunity.
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Affiliation(s)
- Tuan Minh Tran
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhiming Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander Triebl
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sangeeta Nath
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
- Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore, India
| | - Yingying Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ben-Qiang Gong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiao Han
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Junqi Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jian-Feng Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Markus R Wenk
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Satyajit Mayor
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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41
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Tran TM, Ma Z, Triebl A, Nath S, Cheng Y, Gong BQ, Han X, Wang J, Li JF, Wenk MR, Torta F, Mayor S, Yang L, Miao Y. The bacterial quorum sensing signal DSF hijacks Arabidopsis thaliana sterol biosynthesis to suppress plant innate immunity. Life Sci Alliance 2020. [PMID: 32788227 DOI: 10.1101/927731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Quorum sensing (QS) is a recognized phenomenon that is crucial for regulating population-related behaviors in bacteria. However, the direct specific effect of QS molecules on host biology is largely understudied. In this work, we show that the QS molecule DSF (cis-11-methyl-dodecenoic acid) produced by Xanthomonas campestris pv. campestris can suppress pathogen-associated molecular pattern-triggered immunity (PTI) in Arabidopsis thaliana, mediated by flagellin-induced activation of flagellin receptor FLS2. The DSF-mediated attenuation of innate immunity results from the alteration of FLS2 nanoclusters and endocytic internalization of plasma membrane FLS2. DSF altered the lipid profile of Arabidopsis, with a particular increase in the phytosterol species, which impairs the general endocytosis pathway mediated by clathrin and FLS2 nano-clustering on the plasma membrane. The DSF effect on receptor dynamics and host immune responses could be entirely reversed by sterol removal. Together, our results highlighted the importance of sterol homeostasis to plasma membrane organization and demonstrate a novel mechanism by which pathogenic bacteria use their communicating molecule to manipulate pathogen-associated molecular pattern-triggered host immunity.
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Affiliation(s)
- Tuan Minh Tran
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhiming Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alexander Triebl
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sangeeta Nath
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
- Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore, India
| | - Yingying Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ben-Qiang Gong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiao Han
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Junqi Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Jian-Feng Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Markus R Wenk
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Department of Biochemistry, Singapore Lipidomics Incubator (SLING), Yoo Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Satyajit Mayor
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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42
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Chua XY, Chai YL, Chew WS, Chong JR, Ang HL, Xiang P, Camara K, Howell AR, Torta F, Wenk MR, Hilal S, Venketasubramanian N, Chen CP, Herr DR, Lai MKP. Immunomodulatory sphingosine-1-phosphates as plasma biomarkers of Alzheimer's disease and vascular cognitive impairment. Alzheimers Res Ther 2020; 12:122. [PMID: 32998767 PMCID: PMC7528375 DOI: 10.1186/s13195-020-00694-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND There has been ongoing research impetus to uncover novel blood-based diagnostic and prognostic biomarkers for Alzheimer's disease (AD), vascular dementia (VaD), and related cerebrovascular disease (CEVD)-associated conditions within the spectrum of vascular cognitive impairment (VCI). Sphingosine-1-phosphates (S1Ps) are signaling lipids which act on the S1PR family of cognate G-protein-coupled receptors and have been shown to modulate neuroinflammation, a process known to be involved in both neurodegenerative and cerebrovascular diseases. However, the status of peripheral S1P in AD and VCI is at present unclear. METHODS We obtained baseline bloods from individuals recruited into an ongoing longitudinal cohort study who had normal cognition (N = 80); cognitive impairment, no dementia (N = 160); AD (N = 113); or VaD (N = 31), along with neuroimaging assessments of cerebrovascular diseases. Plasma samples were processed for the measurements of major S1P species: d16:1, d17:1, d18:0, and d18:1, along with pro-inflammatory cytokines interleukin (IL)-6, IL-8, and tumor necrosis factor (TNF). Furthermore, in vitro effects of S1Ps on cytokine expression were also studied in an astrocytoma cell line and in rodent primary astrocytes. RESULTS Of the S1Ps species measured, only d16:1 S1P was significantly reduced in the plasma of VaD, but not AD, patients, while the d18:1 to d16:1 ratios were increased in all cognitive subgroups (CIND, AD, and VaD). Furthermore, d18:1 to d16:1 ratios correlated with levels of IL-6, IL-8, and TNF. In both primary astrocytes and an astroglial cell line, treatment with d16:1 or d18:1 S1P resulted in the upregulation of mRNA transcripts of pro-inflammatory cytokines, with d18:1 showing a stronger effect than d16:1. Interestingly, co-treatment assays showed that the addition of d16:1 reduced the extent of d18:1-mediated gene expression, indicating that d16:1 may function to "fine-tune" the pro-inflammatory effects of d18:1. CONCLUSION Taken together, our data suggest that plasma d16:1 S1P may be useful as a diagnostic marker for VCI, while the d18:1 to d16:1 S1P ratio is an index of dysregulated S1P-mediated immunomodulation leading to chronic inflammation-associated neurodegeneration and cerebrovascular damage.
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Affiliation(s)
- Xin Ying Chua
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore
| | - Yuek Ling Chai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore
- Memory, Aging and Cognition Centre, National University Health Systems, Kent Ridge, Singapore
| | - Wee Siong Chew
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore
| | - Joyce R Chong
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore
- Memory, Aging and Cognition Centre, National University Health Systems, Kent Ridge, Singapore
| | - Hui Li Ang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore
- Cancer Science Institute, National University of Singapore, Kent Ridge, Singapore
| | - Ping Xiang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore
| | - Kaddy Camara
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Amy R Howell
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore
| | - Saima Hilal
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore
- Memory, Aging and Cognition Centre, National University Health Systems, Kent Ridge, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Kent Ridge, Singapore
| | | | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore
- Memory, Aging and Cognition Centre, National University Health Systems, Kent Ridge, Singapore
| | - Deron R Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore.
- Department of Biology, San Diego State University, San Diego, CA, USA.
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, 117597, Singapore.
- Memory, Aging and Cognition Centre, National University Health Systems, Kent Ridge, Singapore.
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43
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Teo G, Chew WS, Burla BJ, Herr D, Tai ES, Wenk MR, Torta F, Choi H. MRMkit: Automated Data Processing for Large-Scale Targeted Metabolomics Analysis. Anal Chem 2020; 92:13677-13682. [PMID: 32930575 DOI: 10.1021/acs.analchem.0c03060] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MRMkit is an open-source software package designed for automated processing of large-scale targeted mass spectrometry-based metabolomics data. With improvements in the automation of sample preparation for LC-MS analysis, a challenging next step is to fully automate the workflow to process raw data and ensure the quality of measurements in large-scale analysis settings. MRMkit capitalizes on the richness of large-sample data in capturing peak shapes and interference patterns of transitions across many samples and delivers fully automated, reproducible peak integration results in a scalable and time-efficient manner. In addition to fast and accurate peak integration, the tool also provides reliable data normalization functions and quality metrics along with visualizations for fast data quality evaluation. In addition, MRMkit learns retention time offset patterns by user-specified compound classes and makes recommendations for peak picking in multimodal ion chromatograms. In summary, MRMkit offers highly consistent and scalable data processing capacity for targeted metabolomics, substantially curtailing the time required to produce the final quantification results after LC-MS analysis.
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Affiliation(s)
- Guoshou Teo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E, Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119228
| | - Wee Siong Chew
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD3, 16 Medical Drive, Level 4, #04-01, Singapore 117600
| | - Bo J Burla
- Singapore Lipidomics Incubator, Life Science Institute, National University of Singapore, 28 Medical Drive, Singapore 117456
| | - Deron Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD3, 16 Medical Drive, Level 4, #04-01, Singapore 117600
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E, Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119228
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Block MD7, 8 Medical Drive, Singapore 117596.,Singapore Lipidomics Incubator, Life Science Institute, National University of Singapore, 28 Medical Drive, Singapore 117456
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Block MD7, 8 Medical Drive, Singapore 117596.,Singapore Lipidomics Incubator, Life Science Institute, National University of Singapore, 28 Medical Drive, Singapore 117456
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E, Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119228
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44
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Kopczynski D, Hentschel A, Coman C, Schebb NH, Hornemann T, Mashek DG, Hartung NM, Shevchuk O, Schött HF, Lorenz K, Torta F, Burla B, Zahedi RP, Sickmann A, Kreutz MR, Ejsing CS, Medenbach J, Ahrends R. Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics. Anal Chem 2020; 92:13672-13676. [PMID: 32865986 PMCID: PMC7586293 DOI: 10.1021/acs.analchem.0c02793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
We
introduce STAMPS, a pathway-centric web service for the development
of targeted proteomics assays. STAMPS guides the user by providing
several intuitive interfaces for a rapid and simplified method design.
Applying our curated framework to signaling and metabolic pathways,
we reduced the average assay development time by a factor of ∼150
and revealed that the insulin signaling is actively controlled by
protein abundance changes in insulin-sensitive and -resistance states.
Although at the current state STAMPS primarily contains mouse data,
it was designed for easy extension with additional organisms.
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Affiliation(s)
- Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
| | - Nils Helge Schebb
- Institute for Food Toxicology, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany.,Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gauss-Strasse 20, 42119 Wuppertal, Germany
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zürich, Wagistrasse 14 Schlieren, 8952 Zürich, Switzerland
| | - Douglas G Mashek
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Minnesota, 401 East River Parkway, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Nicole M Hartung
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gauss-Strasse 20, 42119 Wuppertal, Germany
| | - Olga Shevchuk
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Hans-Frieder Schött
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, 28 Medical Drive, #03-03, Singapore 117456, Singapore
| | - Kristina Lorenz
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, 28 Medical Drive, #03-03, Singapore 117456, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, 28 Medical Drive, #03-03, Singapore 117456, Singapore
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Sainte Catherine Road, Montreal, Quebec H3T 1E2, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Gesundheitscampus 4, 44801 Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, United Kingdom
| | - Michael R Kreutz
- Leibniz Group "Dendritic Organelles and Synaptic Function", University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, ZMNH, Martinistrasse 52, 20251 Hamburg, Germany.,RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestraße 6, 39120 Magdeburg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Leipziger Straße 44, 39120 Magdeburg, Germany
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
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45
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Suresh J, Khor IW, Kaur P, Heng HL, Torta F, Dawe GS, Tai ES, Tolwinski NS. Shared signaling pathways in Alzheimer’s and metabolic disease may point to new treatment approaches. FEBS J 2020; 288:3855-3873. [DOI: 10.1111/febs.15540] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/18/2020] [Accepted: 08/21/2020] [Indexed: 12/18/2022]
Affiliation(s)
| | - Ing Wei Khor
- Department of Medicine Yong Loo Lin School of MedicineNational University of Singapore
| | - Prameet Kaur
- Science Division Yale‐ NUS College Singapore Singapore
| | - Hui Li Heng
- Department of Pharmacology Yong Loo Lin School of Medicine National University of Singapore, and Neurobiology Programme
- Life Sciences Institute National University of Singapore Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Gavin S. Dawe
- Department of Pharmacology Yong Loo Lin School of Medicine National University of Singapore, and Neurobiology Programme
- Life Sciences Institute National University of Singapore Singapore
| | - E Shyong Tai
- Department of Medicine Yong Loo Lin School of MedicineNational University of Singapore
- Division of Endocrinology National University HospitalNational University Health System
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46
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Zhao P, Liu ID, Hodgin JB, Benke PI, Selva J, Torta F, Wenk MR, Endrizzi JA, West O, Ou W, Tang E, Goh DLM, Tay SKH, Yap HK, Loh A, Weaver N, Sullivan B, Larson A, Cooper MA, Alhasan K, Alangari AA, Salim S, Gumus E, Chen K, Zenker M, Hildebrandt F, Saba JD. Responsiveness of sphingosine phosphate lyase insufficiency syndrome to vitamin B6 cofactor supplementation. J Inherit Metab Dis 2020; 43:1131-1142. [PMID: 32233035 PMCID: PMC8072405 DOI: 10.1002/jimd.12238] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/26/2022]
Abstract
Sphingosine-1-phosphate (S1P) lyase is a vitamin B6-dependent enzyme that degrades sphingosine-1-phosphate in the final step of sphingolipid metabolism. In 2017, a new inherited disorder was described caused by mutations in SGPL1, which encodes sphingosine phosphate lyase (SPL). This condition is referred to as SPL insufficiency syndrome (SPLIS) or alternatively as nephrotic syndrome type 14 (NPHS14). Patients with SPLIS exhibit lymphopenia, nephrosis, adrenal insufficiency, and/or neurological defects. No targeted therapy for SPLIS has been reported. Vitamin B6 supplementation has therapeutic activity in some genetic diseases involving B6-dependent enzymes, a finding ascribed largely to the vitamin's chaperone function. We investigated whether B6 supplementation might have activity in SPLIS patients. We retrospectively monitored responses of disease biomarkers in patients supplemented with B6 and measured SPL activity and sphingolipids in B6-treated patient-derived fibroblasts. In two patients, disease biomarkers responded to B6 supplementation. S1P abundance and activity levels increased and sphingolipids decreased in response to B6. One responsive patient is homozygous for an SPL R222Q variant present in almost 30% of SPLIS patients. Molecular modeling suggests the variant distorts the dimer interface which could be overcome by cofactor supplementation. We demonstrate the first potential targeted therapy for SPLIS and suggest that 30% of SPLIS patients might respond to cofactor supplementation.
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Affiliation(s)
- Piming Zhao
- Department of Pediatrics, Division of Hematology/Oncology, University of California, San Francisco, California
| | - Isaac D. Liu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Jeffrey B. Hodgin
- Department of Pathology, University of Michigan Hospitals and Health Center, Ann Arbor, Michigan
| | - Peter I. Benke
- SLING, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jeremy Selva
- SLING, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Federico Torta
- SLING, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Markus R. Wenk
- SLING, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - James A. Endrizzi
- Department of Pediatrics, Division of Hematology/Oncology, University of California, San Francisco, California
| | - Olivia West
- Department of Pediatrics, Division of Hematology/Oncology, University of California, San Francisco, California
| | - Weixing Ou
- Department of Pediatrics, Division of Hematology/Oncology, University of California, San Francisco, California
| | - Emily Tang
- Department of Pediatrics, Division of Hematology/Oncology, University of California, San Francisco, California
| | - Denise Li-Meng Goh
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Stacey Kiat-Hong Tay
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Hui-Kim Yap
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Alwin Loh
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Nicole Weaver
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Bonnie Sullivan
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Division of Clinical Genetics, Children’s Mercy Kansas City, Kansas City, Missouri
- Department of Pediatrics, University of Missouri, Kansas City, Missouri
| | - Austin Larson
- Department of Pediatrics, University of Colorado School of Medicine, Denver, Colorado
| | - Megan A. Cooper
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Khalid Alhasan
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah A. Alangari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Suha Salim
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Evren Gumus
- Department of Medicine, Harran University, Sanliurfa, Turkey
| | - Karin Chen
- Department of Pediatrics, Division of Allergy and Immunology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Martin Zenker
- Institute of Human Genetics, Otto von Guericke University, Magdeburg, Germany
| | | | - Julie D. Saba
- Department of Pediatrics, Division of Hematology/Oncology, University of California, San Francisco, California
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47
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Seah JYH, Chew WS, Torta F, Khoo CM, Wenk MR, Herr DR, Choi H, Tai ES, van Dam RM. Plasma sphingolipids and risk of cardiovascular diseases: a large-scale lipidomic analysis. Metabolomics 2020; 16:89. [PMID: 32816082 DOI: 10.1007/s11306-020-01709-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 08/10/2020] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Sphingolipids are a diverse class of lipids with various roles in cell functions and subclasses such as ceramides have been associated with cardiovascular diseases (CVD) in previous studies. OBJECTIVES We aimed to measure molecularly-distinct sphingolipids via a large-scale lipidomic analysis and expand the literature to an Asian population. METHODS We performed a lipidomics evaluation of 79 molecularly distinct sphingolipids in the plasma of 2627 ethnically-Chinese Singaporeans. RESULTS During a mean follow-up of 12.9 years, we documented 152 cases of major CVD (non-fatal myocardial infarction, stroke and cardiovascular death). Total ceramide concentrations were not associated with CVD risk [hazard ratio (HR), 0.99; 95% CI 0.81-1.21], but higher circulating total monohexosylceramides (HR, 1.22; 95% CI 1.03, 1.45), total long-chain sphingolipids (C16-C18) (HR, 1.22; 95% CI 1.02, 1.45) and total 18:1 sphingolipids (HR, 1.21; 95% CI 1.01, 1.46) were associated with higher CVD risk after adjusting for conventional CVD risk factors. CONCLUSIONS Our results do not support the hypothesis that higher ceramide concentrations are linked to higher CVD risk, but suggest that other classes of sphingolipids may affect CVD risk.
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Affiliation(s)
- Jowy Yi Hoong Seah
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), 12 Science Drive 2, #10-01, Singapore, 117549, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, NUS, Singapore, 119077, Singapore.
| | - Wee Siong Chew
- Department of Pharmacology, Yong Loo Lin School of Medicine, NUS, Singapore, 117600, Singapore
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore, 117596, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore, 117456, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, NUS and National University Health System, Singapore, 119228, Singapore
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, Singapore, 117596, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, NUS, Singapore, 117456, Singapore
- Department of Biological Sciences, Faculty of Science, NUS, Singapore, 117558, Singapore
| | - Deron R Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, NUS, Singapore, 117600, Singapore
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), 12 Science Drive 2, #10-01, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, NUS and National University Health System, Singapore, 119228, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore, 138673, Singapore
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), 12 Science Drive 2, #10-01, Singapore, 117549, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, NUS and National University Health System, Singapore, 119228, Singapore
- Duke-NUS Graduate Medical School, Singapore, 169857, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore (NUS), 12 Science Drive 2, #10-01, Singapore, 117549, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, NUS, Singapore, 119077, Singapore.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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48
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Chan KWK, Watanabe S, Jin JY, Pompon J, Teng D, Alonso S, Vijaykrishna D, Halstead SB, Marzinek JK, Bond PJ, Burla B, Torta F, Wenk MR, Ooi EE, Vasudevan SG. A T164S mutation in the dengue virus NS1 protein is associated with greater disease severity in mice. Sci Transl Med 2020; 11:11/498/eaat7726. [PMID: 31243154 DOI: 10.1126/scitranslmed.aat7726] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 10/11/2018] [Accepted: 12/03/2018] [Indexed: 12/14/2022]
Abstract
Dengue viruses cause severe and sudden human epidemics worldwide. The secreted form of the nonstructural protein 1 (sNS1) of dengue virus causes vascular leakage, a hallmark of severe dengue disease. Here, we reverse engineered the T164S mutation of NS1, associated with the severity of dengue epidemics in the Americas, into a dengue virus serotype 2 mildly infectious strain. The T164S mutant virus decreased infectious virus production and increased sNS1 production in mammalian cell lines and human peripheral blood mononuclear cells (PBMCs) without affecting viral RNA replication. Gene expression profiling of 268 inflammation-associated human genes revealed up-regulation of genes induced in response to vascular leakage. Infection of the mosquito vector Aedes aegypti with the T164S mutant virus resulted in increased viral load in the mosquito midgut and higher sNS1 production compared to wild-type virus infection. Infection of type 1 and 2 interferon receptor-deficient AG129 mice with the T164S mutant virus resulted in severe disease coupled with increased complement activation, tissue inflammation, and more rapid mortality compared to AG129 mice infected with wild-type virus. Molecular dynamics simulations predicted that mutant sNS1 formed stable dimers similar to the wild-type protein, whereas the hexameric mutant sNS1 was predicted to be unstable. Immunoaffinity-purified sNS1 from T164S mutant virus-infected mammalian cells was associated with different lipid classes compared to wild-type sNS1. Treatment of human PBMCs with sNS1 purified from T164S mutant virus resulted in a twofold higher production of proinflammatory cytokines, suggesting a mechanism for how mutant sNS1 may cause more severe dengue disease.
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Affiliation(s)
- Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Department of Microbiology and Immunology, 5 Science Drive 2, Singapore 117545, Singapore
| | - Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jocelyn Y Jin
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Julien Pompon
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,MIVEGEC, UMR IRD 224-CNRS5290 Université de Montpellier, Montpellier, France
| | - Don Teng
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia
| | - Sylvie Alonso
- Department of Microbiology and Immunology, 5 Science Drive 2, Singapore 117545, Singapore.,Immunology Programme, Life Science Institute, National University of Singapore, Singapore 117456, Singapore
| | - Dhanasekaran Vijaykrishna
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia
| | - Scott B Halstead
- Department of Preventive Medicine and Biometrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20817, USA
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis St., Singapore 138671, Singapore
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), 30 Biopolis St., Singapore 138671, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Department of Microbiology and Immunology, 5 Science Drive 2, Singapore 117545, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore. .,Department of Microbiology and Immunology, 5 Science Drive 2, Singapore 117545, Singapore
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Ambaw YA, Wong T, Chong R, Ah H, Ji S, Raida M, Torta F, Wenk MR, Tong L. Change of tear lipid mediators in a post-trabeculectomy cohort. Ocul Surf 2020; 18:565-574. [PMID: 32622916 DOI: 10.1016/j.jtos.2020.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/02/2020] [Accepted: 06/06/2020] [Indexed: 11/18/2022]
Abstract
PURPOSE Trabeculectomy surgery could affect ocular surface disease (OSD) in several ways, through cessation of long term glaucoma eyedrops, exposure to operative mitomycin C and post-operative eyedrops including corticosteroids and aminoglycosides and reduction in eyelid hygiene measures. Previously we showed the relevance of tear lipid mediators (also referred oxylipins) in OSD. Here, we aim to evaluate changes of these lipids in a post-trabeculectomy cohort. METHODS Patients undergoing trabeculectomy were prospectively evaluated and had tear collected using Schirmer's strips, preoperatively and postoperatively at 0.5, 1.0 and 3.0 years. Lipid mediators were analyzed using liquid chromatography mass spectrometry. RESULTS The normalized concentrations of 40 lipid mediators were between 0.1 and 8.0 ng/mL, whereas docosahexaenoic acid (DHA), Arachidonic acid (AA) and eicosapentaenoic acid (EPA) ranged up to a few hundred ng/mL. The concentrations of lipid mediators, except DHA, EPA, and thromboxane (TXB1), showed reduction after surgery. At the last visit, these lipids were significantly reduced by 1/3 to ½, compared to pre-operative values: 8-HETE, 15-HETE, 15-oxoETE, 11-HDoHE, 17-HDoHE, and 20-OH-LTB4. To examine collective changes of lipids, clustering analysis revealed 10 groups of lipids consistent with known metabolic pathways. RESULTS An increase in the level of 2,3-dinor-8-isoPGF2α between 0 and 0.5 year was associated with inferior corneal staining at 0.5 year. In 14 patients who required post-operative needling, six lipid mediators were found to be significantly higher at 1.0 year compared to non-needled patients. CONCLUSIONS In this 3-years study, trabeculectomy reduced the tear level of pro-inflammatory lipid mediators. Patients who required needling of the bleb to maintain surgical success may have a chronic underlying inflammatory process associated with fibrosis.
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Affiliation(s)
- Yohannes Abere Ambaw
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore; Department of Molecular Metabolism, Harvard T.H Chan School of Public Health, Harvard Univeristy, USA.
| | - Tina Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Cornea and External Eye Disease, Singapore National Eye Center, Singapore; Ocular Surface Research Group, Singapore Eye Research Institute, Singapore; Eye-Academic Clinical Program, Duke-NUS Medical School, Singapore; School of Material Science and Engineering, Nanyang Technological University, Singapore.
| | - Rachel Chong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Glaucoma, Singapore National Eye Center, Singapore
| | - Hou Ah
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Ocular Surface Research Group, Singapore Eye Research Institute, Singapore
| | - Shanshan Ji
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Manfred Raida
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Louis Tong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Cornea and External Eye Disease, Singapore National Eye Center, Singapore; Ocular Surface Research Group, Singapore Eye Research Institute, Singapore; Eye-Academic Clinical Program, Duke-NUS Medical School, Singapore.
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50
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Carrat GR, Haythorne E, Tomas A, Haataja L, Müller A, Arvan P, Piunti A, Cheng K, Huang M, Pullen TJ, Georgiadou E, Stylianides T, Amirruddin NS, Salem V, Distaso W, Cakebread A, Heesom KJ, Lewis PA, Hodson DJ, Briant LJ, Fung AC, Sessions RB, Alpy F, Kong AP, Benke PI, Torta F, Teo AKK, Leclerc I, Solimena M, Wigley DB, Rutter GA. The type 2 diabetes gene product STARD10 is a phosphoinositide-binding protein that controls insulin secretory granule biogenesis. Mol Metab 2020; 40:101015. [PMID: 32416313 PMCID: PMC7322359 DOI: 10.1016/j.molmet.2020.101015] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/24/2020] [Accepted: 05/05/2020] [Indexed: 02/09/2023] Open
Abstract
OBJECTIVE Risk alleles for type 2 diabetes at the STARD10 locus are associated with lowered STARD10 expression in the β-cell, impaired glucose-induced insulin secretion, and decreased circulating proinsulin:insulin ratios. Although likely to serve as a mediator of intracellular lipid transfer, the identity of the transported lipids and thus the pathways through which STARD10 regulates β-cell function are not understood. The aim of this study was to identify the lipids transported and affected by STARD10 in the β-cell and the role of the protein in controlling proinsulin processing and insulin granule biogenesis and maturation. METHODS We used isolated islets from mice deleted selectively in the β-cell for Stard10 (βStard10KO) and performed electron microscopy, pulse-chase, RNA sequencing, and lipidomic analyses. Proteomic analysis of STARD10 binding partners was executed in the INS1 (832/13) cell line. X-ray crystallography followed by molecular docking and lipid overlay assay was performed on purified STARD10 protein. RESULTS βStard10KO islets had a sharply altered dense core granule appearance, with a dramatic increase in the number of "rod-like" dense cores. Correspondingly, basal secretion of proinsulin was increased versus wild-type islets. The solution of the crystal structure of STARD10 to 2.3 Å resolution revealed a binding pocket capable of accommodating polyphosphoinositides, and STARD10 was shown to bind to inositides phosphorylated at the 3' position. Lipidomic analysis of βStard10KO islets demonstrated changes in phosphatidylinositol levels, and the inositol lipid kinase PIP4K2C was identified as a STARD10 binding partner. Also consistent with roles for STARD10 in phosphoinositide signalling, the phosphoinositide-binding proteins Pirt and Synaptotagmin 1 were amongst the differentially expressed genes in βStard10KO islets. CONCLUSION Our data indicate that STARD10 binds to, and may transport, phosphatidylinositides, influencing membrane lipid composition, insulin granule biosynthesis, and insulin processing.
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Affiliation(s)
- Gaelle R. Carrat
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK
| | - Elizabeth Haythorne
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK
| | - Leena Haataja
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany,Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich, University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany,Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Peter Arvan
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alexandra Piunti
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK,Lille 1 University-Science and Technology, Cité Scientifique, 59655, Villeneuve d'Ascq Cedex, France
| | - Kaiying Cheng
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
| | - Mutian Huang
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK
| | - Timothy J. Pullen
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK,Department of Diabetes, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Eleni Georgiadou
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK
| | - Theodoros Stylianides
- Loughborough University, Centre of Innovative and Collaborative Construction Engineering, Leicestershire, LE11 3TU, UK
| | - Nur Shabrina Amirruddin
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A∗STAR, Proteos, Singapore, 138673, Singapore,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Victoria Salem
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK,Section of Investigative Medicine, Department of Medicine, Imperial College London, du Cane Road, London, W12 0NN, UK
| | - Walter Distaso
- Imperial College Business School, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Andrew Cakebread
- London Metallomics Facility, King's College London, Strand, London, WC2R 2LS, UK
| | | | | | - David J. Hodson
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK,Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, UK,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Midlands, UK
| | - Linford J. Briant
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Annie C.H. Fung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Richard B. Sessions
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Fabien Alpy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Centre National de la Recherche Scientifique (CNRS), UMR 7104, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Alice P.S. Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Peter I. Benke
- Singapore Lipidomics Incubator, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Mdical Drive, Singapore, 117596, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Mdical Drive, Singapore, 117596, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), A∗STAR, Proteos, Singapore, 138673, Singapore,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Isabelle Leclerc
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany,Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich, University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany,Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Dale B. Wigley
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Imperial College London, du Cane Road, London, W12 0NN, UK,Corresponding author. +44 (0)20 7594 3340.
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