1
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Nilsson JM, Balgoma D, Pettersson C, Lennernäs H, Heindryckx F, Hedeland M. Ammonium bicarbonate buffers combined with hybrid surface technology columns improve the peak shape of strongly tailing lipids. Anal Chim Acta 2024; 1316:342811. [PMID: 38969401 DOI: 10.1016/j.aca.2024.342811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Lipids such as phosphatidic acids (PAs) and cardiolipins (CLs) present strongly tailing peaks in reversed phase liquid chromatography, which entails low detectability. They are usually analyzed by hydrophilic interaction liquid chromatography (HILIC), which hampers high-throughput lipidomics. Thus, there is a great need for improved analytical methods in order to obtain a broader coverage of the lipidome in a single chromatographic method. We investigated the effect of ammonium bicarbonate (ABC) on peak asymmetry and detectability, in comparison with ammonium formate (AFO) on both a conventional BEH C18 column and an HST-CSH C18 column. RESULTS The combination of 2.5 mM ABC buffer pH 8 with an HST-CSH C18 column produced significantly improved results, reducing the asymmetry factor at 10 % peak height of PA 16:0/18:1 from 8.4 to 1.6. Furthermore, on average, there was up to a 54-fold enhancement in the peak height of its [M - H]- ion compared to AFO and the BEH C18 column. We confirmed this beneficial effect on other strongly tailing lipids, with accessible phosphate moieties e.g., cardiolipins, phosphatidylinositol phosphate, phosphatidylinositol bisphosphate, phosphorylated ceramide and phosphorylated sphingosine. Furthermore, we found an increased detectability of phospho- and sphingolipids up to 28 times in negative mode when using an HST-CSH C18 column. The method was successfully applied to mouse liver samples, where previously undetected endogenous phospholipids could be analyzed with improved chromatographic separation. SIGNIFICANCE In conclusion, the use of 2.5 mM ABC substantially improved the peak shape of PAs and enhanced the detectability of the lipidome in negative mode on an RPLC-ESI-Q-TOF-MS system on both BEH C18 and HST-CSH C18 columns. This method provides a wider coverage of the lipidome with one single injection for future lipidomic applications in negative mode.
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Affiliation(s)
- Jenny M Nilsson
- Department of Medicinal Chemistry, Uppsala Biomedical Centre, Uppsala University, Box 574, 75123 Uppsala, Sweden
| | - David Balgoma
- Department of Medicinal Chemistry, Uppsala Biomedical Centre, Uppsala University, Box 574, 75123 Uppsala, Sweden; Instituto de Biomedicina y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, C/ Sanz y Forés 3, 47003, Valladolid, Spain
| | - Curt Pettersson
- Department of Medicinal Chemistry, Uppsala Biomedical Centre, Uppsala University, Box 574, 75123 Uppsala, Sweden
| | - Hans Lennernäs
- Department of Pharmaceutical Biosciences, Uppsala Biomedical Centre, Uppsala University, Box 591, 75123 Uppsala, Sweden
| | - Femke Heindryckx
- Department of Medical Cell Biology, Uppsala Biomedical Centre, Uppsala University, Box 571, 75123 Uppsala, Sweden
| | - Mikael Hedeland
- Department of Medicinal Chemistry, Uppsala Biomedical Centre, Uppsala University, Box 574, 75123 Uppsala, Sweden.
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2
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Burla B, Oh J, Nowak A, Piraud N, Meyer E, Mei D, Bendt AK, Studt JD, Frey BM, Torta F, Wenk MR, Krayenbuehl PA. Plasma and platelet lipidome changes in Fabry disease. Clin Chim Acta 2024; 562:119833. [PMID: 38955246 DOI: 10.1016/j.cca.2024.119833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Fabry disease (FD) is an X-linked lysosomal storage disorder characterized by the progressive accumulation of globotriaosylceramide (Gb3) leading to systemic manifestations such as chronic kidney disease, cardiomyopathy, and stroke. There is still a need for novel markers for improved FD screening and prognosis. Moreover, the pathological mechanisms in FD, which also include systemic inflammation and fibrosis, are not yet fully understood. METHODS Plasma and platelets were obtained from 11 ERT (enzyme-replacement therapy)-treated symptomatic, 4 asymptomatic FD patients, and 13 healthy participants. A comprehensive targeted lipidomics analysis was conducted quantitating more than 550 lipid species. RESULTS Sphingadiene (18:2;O2)-containing sphingolipid species, including Gb3 and galabiosylceramide (Ga2), were significantly increased in FD patients. Plasma levels of lyso-dihexosylceramides, sphingoid base 1-phosphates (S1P), and GM3 ganglioside were also altered in FD patients, as well as specific plasma ceramide ratios used in cardiovascular disease risk prediction. Gb3 did not increase in patients' platelets but displayed a high inter-individual variability in patients and healthy participants. Platelets accumulated, however, lyso-Gb3, acylcarnitines, C16:0-sphingolipids, and S1P. CONCLUSIONS This study identified lipidome changes in plasma and platelets from FD patients, a possible involvement of platelets in FD, and potential new markers for screening and monitoring of this disease.
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Affiliation(s)
- Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore.
| | - Jeongah Oh
- Precision Medicine Translational Research Program and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.
| | - Albina Nowak
- Department of Internal Medicine, Psychiatric University Clinic Zurich, Switzerland; Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich, Switzerland.
| | | | - Eduardo Meyer
- Swiss Red Cross (SRC), Zurich-Schlieren, Switzerland
| | - Ding Mei
- Precision Medicine Translational Research Program and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anne K Bendt
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Jan-Dirk Studt
- Division of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Beat M Frey
- Swiss Red Cross (SRC), Zurich-Schlieren, Switzerland
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore; Precision Medicine Translational Research Program and Department of Biochemistry, 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 and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Pierre-Alexandre Krayenbuehl
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich, Switzerland; General Practice Brauereistrasse, Uster-Zurich, Switzerland.
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3
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Gurung RL, M Y, Tham WK, Liu S, Zheng H, Lee J, Ang K, Wenk M, Subramaniam T, Sum CF, Torta F, Liu JJ, Lim SC. Association of plasma ceramide with decline in kidney function in patients with type 2 diabetes. J Lipid Res 2024; 65:100552. [PMID: 38704028 PMCID: PMC11176756 DOI: 10.1016/j.jlr.2024.100552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Circulating ceramide levels are dysregulated in kidney disease. However, their associations with rapid decline in kidney function (RDKF) and end-stage kidney disease (ESKD) in patients with type 2 diabetes (T2D) are unknown. In this prospective study of 1746 T2D participants, we examined the association of plasma ceramide Cer16:0, Cer18:0, Cer24:0, and Cer24:1 with RDKF, defined as an estimated glomerular filtration rate (eGFR) decline of 5 ml/min/1.73 m2 per year or greater, and ESKD defined as eGFR <15/min/1.73 m2 for at least 3 months, on dialysis or renal death at follow-up. During a median follow-up period of 7.7 years, 197 patients experienced RDKF. Ceramide Cer24:0 (odds ratio [OR] = 0.71, 95% CI 0.56-0.90) and ratios Cer16:0/Cer24:0 (OR = 3.54 [1.70-7.35]), Cer18:0/Cer24:0 (OR = 1.89 [1.10-3.25]), and Cer24:1/Cer24:0 (OR = 4.01 [1.93-8.31]) significantly associated with RDKF in multivariable analysis; 124 patients developed ESKD. The ratios Cer16:0/Cer24:0 (hazard ratio [HR] = 3.10 [1.44-6.64]) and Cer24:1/Cer24:0 (HR = 4.66 [1.93-11.24]) significantly associated with a higher risk of ESKD. The Cer24:1/Cer24:0 ratio improved risk discrimination for ESKD beyond traditional risk factors by small but statistically significant margin (Harrell C-index difference: 0.01; P = 0.022). A high ceramide risk score also associated with RDKF (OR = 2.28 [1.26-4.13]) compared to lower risk score. In conclusion, specific ceramide levels and their ratios are associated with RDKF and conferred an increased risk of ESKD, independently of traditional risk factors, including baseline renal functions in patients with T2D.
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Affiliation(s)
- Resham L Gurung
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore; Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Yiamunaa M
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Wai Kin Tham
- 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
| | - Sylvia Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Huili Zheng
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Janus Lee
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Keven Ang
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Markus 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
| | | | - Chee Fang Sum
- Diabetes Centre, Admiralty Medical Centre, 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
| | - Jian-Jun Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore, Singapore; Diabetes Centre, Admiralty Medical Centre, Singapore, Singapore; Saw Swee Hock School of Public Health, Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
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4
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Kulyk DS, Baryshnikov GV, Damale PS, Maher S, Badu-Tawiah AK. Charge inversion under plasma-nanodroplet reaction conditions excludes Fischer esterification for unsaturated fatty acids: a chemical approach for type II isobaric overlap. Chem Sci 2024; 15:914-922. [PMID: 38239686 PMCID: PMC10793210 DOI: 10.1039/d3sc05369e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/10/2023] [Indexed: 01/22/2024] Open
Abstract
Direct infusion ionization methods provide the highest throughput strategy for mass spectrometry (MS) analysis of low-volume samples. But the trade-off includes matrix effects, which can significantly reduce analytical performance. Herein, we present a novel chemical approach to tackle a special type of matrix effect, namely type II isobaric overlap. We focus on detailed investigation of a nanodroplet-based esterification chemistry for differentiating isotopologue [M + 2] signal due to unsaturated fatty acid (FA) from the monoisotopic signal from a saturated FA. The method developed involves the online fusion of nonthermal plasma with charged nanodroplets, enabling selective esterification of saturated FAs. We discovered that unsaturated FAs undergo spontaneous intramolecular reaction via a novel mechanism based on a carbocation intermediate to afford a protonated lactone moiety (resonance stabilized cyclic carbonium ion), whose mass is the same as the original protonated unsaturated FA. Therefore, the monoisotopic signal from any saturated FA can be selectively shifted away from the mass-to-charge position where the isobaric interference occurs to enable effective characterization by MS. The mechanism governing the spontaneous intramolecular reactions for unsaturated FAs was validated with DFT calculations, experimentation with standards, and isotope labeling. This novel insight achieved via the ultrafast plasma-nanodroplet reaction environment provides a potentially useful synthetic pathway to achieve catalyst-free lactone preparation. Analytically, we believe the performance of direct infusion MS can be greatly enhanced by combining our approach with prior sample enrichment steps for applications in biomedicine and food safety. Also, combination with portable mass spectrometers can improve the efficiency of field studies since front-end separation is not possible under such conditions.
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Affiliation(s)
- Dmytro S Kulyk
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Ave. Columbus OH 43210 USA
| | - Glib V Baryshnikov
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University SE-60174 Norrköping Sweden
| | - Purva S Damale
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Ave. Columbus OH 43210 USA
| | - Simon Maher
- Department of Electrical Engineering and Electronics, University of Liverpool Liverpool UK
| | - Abraham K Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Ave. Columbus OH 43210 USA
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5
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Zhang Z, Singh M, Kindt A, Wegrzyn AB, Pearson MJ, Ali A, Harms AC, Baker P, Hankemeier T. Development of a targeted hydrophilic interaction liquid chromatography-tandem mass spectrometry based lipidomics platform applied to a coronavirus disease severity study. J Chromatogr A 2023; 1708:464342. [PMID: 37696124 DOI: 10.1016/j.chroma.2023.464342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
The importance of lipids seen in studies of metabolism, cancer, the recent COVID-19 pandemic and other diseases has brought the field of lipidomics to the forefront of clinical research. Quantitative and comprehensive analysis is required to understand biological interactions among lipid species. However, lipidomic analysis is often challenging due to the various compositional structures, diverse physicochemical properties, and wide dynamic range of concentrations of lipids in biological systems. To study the comprehensive lipidome, a hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS)-based screening method with 1200 lipid features across 19 (sub)classes, including both nonpolar and polar lipids, has been developed. HILIC-MS/MS was selected due to its class separation property and fatty acyl chain level information. 3D models of class chromatographic retention behavior were established and evaluations of cross-class and within-class interferences were performed to avoid over-reporting these features. This targeted HILIC-MS/MS method was fully validated, with acceptable analytical parameters in terms of linearity, precision, reproducibility, and recovery. The accurate quantitation of 608 lipid species in the SRM 1950 NIST plasma was achieved using multi-internal standards per class and post-hoc correction, extending current databases by providing lipid concentrations resolved at fatty acyl chain level. The overall correlation coefficients (R2) of measured concentrations with values from literature range from 0.64 to 0.84. The applicability of the developed targeted lipidomics method was demonstrated by discovering 520 differential lipid features related to COVID-19 severity. This high coverage and targeted approach will aid in future investigations of the lipidome in various disease contexts.
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Affiliation(s)
- Zhengzheng Zhang
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Madhulika Singh
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Alida Kindt
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Agnieszka B Wegrzyn
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | | | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Amy C Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | | | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
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6
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Liu Z, Rochfort S. Lipidomics in milk: recent advances and developments. Curr Opin Food Sci 2023. [DOI: 10.1016/j.cofs.2023.101016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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7
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Medina J, Borreggine R, Teav T, Gao L, Ji S, Carrard J, Jones C, Blomberg N, Jech M, Atkins A, Martins C, Schmidt-Trucksass A, Giera M, Cazenave-Gassiot A, Gallart-Ayala H, Ivanisevic J. Omic-Scale High-Throughput Quantitative LC-MS/MS Approach for Circulatory Lipid Phenotyping in Clinical Research. Anal Chem 2023; 95:3168-3179. [PMID: 36716250 DOI: 10.1021/acs.analchem.2c02598] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Lipid analysis at the molecular species level represents a valuable opportunity for clinical applications due to the essential roles that lipids play in metabolic health. However, a comprehensive and high-throughput lipid profiling remains challenging given the lipid structural complexity and exceptional diversity. Herein, we present an 'omic-scale targeted LC-MS/MS approach for the straightforward and high-throughput quantification of a broad panel of complex lipid species across 26 lipid (sub)classes. The workflow involves an automated single-step extraction with 2-propanol, followed by lipid analysis using hydrophilic interaction liquid chromatography in a dual-column setup coupled to tandem mass spectrometry with data acquisition in the timed-selective reaction monitoring mode (12 min total run time). The analysis pipeline consists of an initial screen of 1903 lipid species, followed by high-throughput quantification of robustly detected species. Lipid quantification is achieved by a single-point calibration with 75 isotopically labeled standards representative of different lipid classes, covering lipid species with diverse acyl/alkyl chain lengths and unsaturation degrees. When applied to human plasma, 795 lipid species were measured with median intra- and inter-day precisions of 8.5 and 10.9%, respectively, evaluated within a single and across multiple batches. The concentration ranges measured in NIST plasma were in accordance with the consensus intervals determined in previous ring-trials. Finally, to benchmark our workflow, we characterized NIST plasma materials with different clinical and ethnic backgrounds and analyzed a sub-set of sera (n = 81) from a clinically healthy elderly population. Our quantitative lipidomic platform allowed for a clear distinction between different NIST materials and revealed the sex-specificity of the serum lipidome, highlighting numerous statistically significant sex differences.
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Affiliation(s)
- Jessica Medina
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL-CHUV, Rue du Bugnon 19, Lausanne CH-1005, Switzerland
| | - Rebecca Borreggine
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL-CHUV, Rue du Bugnon 19, Lausanne CH-1005, Switzerland
| | - Tony Teav
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL-CHUV, Rue du Bugnon 19, Lausanne CH-1005, Switzerland
| | - Liang Gao
- Department of Biochemistry and Precision Medicine TRP, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore.,Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Shanshan Ji
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Justin Carrard
- Division of Sports and Exercise Medicine, Department of Sport, Exercise and Health, University of Basel, Birsstrasse 320B, Basel CH-4052, Switzerland
| | - Christina Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Niek Blomberg
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands
| | - Martin Jech
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Alan Atkins
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Claudia Martins
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Arno Schmidt-Trucksass
- Division of Sports and Exercise Medicine, Department of Sport, Exercise and Health, University of Basel, Birsstrasse 320B, Basel CH-4052, Switzerland
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333ZA, Netherlands
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry and Precision Medicine TRP, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore.,Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL-CHUV, Rue du Bugnon 19, Lausanne CH-1005, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL-CHUV, Rue du Bugnon 19, Lausanne CH-1005, Switzerland
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8
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Zhang D, Lin Q, Xia T, Zhao J, Zhang W, Ouyang Z, Xia Y. LipidOA: A Machine-Learning and Prior-Knowledge-Based Tool for Structural Annotation of Glycerophospholipids. Anal Chem 2022; 94:16759-16767. [DOI: 10.1021/acs.analchem.2c03505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Donghui Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing100084, China
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing10084, China
| | - Qiaohong Lin
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing10084, China
| | - Tian Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing10084, China
| | - Jing Zhao
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing10084, China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing100084, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing10084, China
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9
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Hasan Z, Nguyen TQ, Lam BWS, Wong JHX, Wong CCY, Tan CKH, Yu J, Thiam CH, Zhang Y, Angeli V, Nguyen LN. Postnatal deletion of Spns2 prevents neuroinflammation without compromising blood vascular functions. Cell Mol Life Sci 2022; 79:541. [PMID: 36198832 DOI: 10.1007/s00018-022-04573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/09/2022] [Accepted: 09/27/2022] [Indexed: 11/03/2022]
Abstract
Protein Spinster homolog 2 (Spns2) is a sphingosine-1-phosphate (S1P) transporter that releases S1P to regulate lymphocyte egress and trafficking. Global deletion of Spns2 (Spns2-/-) has been shown to reduce disease severity in several autoimmune disease models. To examine whether Spns2 could be exploited as a drug target, we generated and characterized the mice with postnatal knockout of Spns2 (Spns2-Mx1Cre). Our results showed that Spns2-Mx1Cre mice had significantly low number of lymphocytes in blood and lymphoid organs similar to Spns2-/- mice. Lymph but not plasma S1P levels were significantly reduced in both groups of knockout mice. Our lipidomic results also showed that Spns2 releases different S1P species into lymph. Interestingly, lymphatic vessels in the lymph nodes (LNs) of Spns2-/- and Spns2-Mx1Cre mice exhibited morphological defects. The structures of high endothelial venules (HEV) in the LNs of Spns2-Mx1Cre mice were disorganized. These results indicate that lack of Spns2 affects both S1P secretion and LN vasculatures. Nevertheless, blood vasculature of these Spns2 deficient mice was not different to controls under homeostasis and vascular insults. Importantly, Spns2-Mx1Cre mice were resistant to multiple sclerosis in experimental autoimmune encephalomyelitis (EAE) models with significant reduction of pathogenic Th17 cells in the central nervous system (CNS). This study suggests that pharmacological inhibition of Spns2 may be exploited for therapeutic applications in treatment of neuroinflammation.
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Affiliation(s)
- Zafrul Hasan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Toan Q Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Brenda Wan Shing Lam
- Department of Pharmacology, Institute for Digital Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 16 Medical Drive, Singapore, Singapore
| | - Jovi Hui Xin Wong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Caleb Cheng Yi Wong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Clarissa Kai Hui Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Jiabo Yu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Life Sciences Institute, Immunology Program, National University of Singapore, Singapore, 117456, Singapore.,Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Chung Hwee Thiam
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Life Sciences Institute, Immunology Program, National University of Singapore, Singapore, 117456, Singapore.,Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Yongliang Zhang
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Life Sciences Institute, Immunology Program, National University of Singapore, Singapore, 117456, Singapore.,Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Veronique Angeli
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Life Sciences Institute, Immunology Program, National University of Singapore, Singapore, 117456, Singapore.,Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Long N Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore. .,Life Sciences Institute, Singapore Lipidomics Incubator (SLING), National University of Singapore, Singapore, 117456, Singapore. .,Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore. .,Life Sciences Institute, Immunology Program, National University of Singapore, Singapore, 117456, Singapore. .,Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore.
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10
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Transient Complexity of E. coli Lipidome Is Explained by Fatty Acyl Synthesis and Cyclopropanation. Metabolites 2022; 12:metabo12090784. [PMID: 36144187 PMCID: PMC9500627 DOI: 10.3390/metabo12090784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/04/2022] Open
Abstract
In the case of many bacteria, such as Escherichia coli, the composition of lipid molecules, termed the lipidome, temporally adapts to different environmental conditions and thus modifies membrane properties to permit growth and survival. Details of the relationship between the environment and lipidome composition are lacking, particularly for growing cultures under either favourable or under stress conditions. Here, we highlight compositional lipidome changes by describing the dynamics of molecular species throughout culture-growth phases. We show a steady cyclopropanation of fatty acyl chains, which acts as a driver for lipid diversity. There is a bias for the cyclopropanation of shorter fatty acyl chains (FA 16:1) over longer ones (FA 18:1), which likely reflects a thermodynamic phenomenon. Additionally, we observe a nearly two-fold increase in saturated fatty acyl chains in response to the presence of ampicillin and chloramphenicol, with consequences for membrane fluidity and elasticity, and ultimately bacterial stress tolerance. Our study provides the detailed quantitative lipidome composition of three E. coli strains across culture-growth phases and at the level of the fatty acyl chains and provides a general reference for phospholipid composition changes in response to perturbations. Thus, lipidome diversity is largely transient and the consequence of lipid synthesis and cyclopropanation.
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11
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Le TNU, Nguyen TQ, Kalailingam P, Nguyen YTK, Sukumar VK, Tan CKH, Tukijan F, Couty L, Hasan Z, Del Gaudio I, Wenk MR, Cazenave-Gassiot A, Camerer E, Nguyen LN. Mfsd2b and Spns2 are essential for maintenance of blood vessels during development and in anaphylactic shock. Cell Rep 2022; 40:111208. [PMID: 35977478 DOI: 10.1016/j.celrep.2022.111208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 05/23/2022] [Accepted: 07/21/2022] [Indexed: 01/22/2023] Open
Abstract
Sphingosine-1-phosphate (S1P) is a potent lipid mediator that is secreted by several cell types. We recently showed that Mfsd2b is an S1P transporter from hematopoietic cells that contributes approximately 50% plasma S1P. Here we report the characterization of compound deletion of Mfsd2b and Spns2, another S1P transporter active primarily in endothelial cells. Global deletion of Mfsd2b and Spns2 (global double knockout [gDKO]) results in embryonic lethality beyond embryonic day 14.5 (E14.5), with severe hemorrhage accompanied by defects of tight junction proteins, indicating that Mfsd2b and Spns2 provide S1P for signaling, which is essential for blood vessel integrity. Compound postnatal deletion of Mfsd2b and Spns2 using Mx1Cre (ctDKO-Mx1Cre) results in maximal 80% reduction of plasma S1P. ctDKO-Mx1Cre mice exhibit severe susceptibility to anaphylaxis, indicating that S1P from Mfsd2b and Spns2 is indispensable for vascular homeostasis. Our results show that S1P export from Mfsd2b and Spns2 is essential for developing and mature vasculature.
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Affiliation(s)
- Thanh Nha Uyen Le
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Toan Q Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Pazhanichamy Kalailingam
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Yen Thi Kim Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Viresh Krishnan Sukumar
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Clarissa Kai Hui Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Farhana Tukijan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Ludovic Couty
- Université Paris Cité, PARCC, INSERM U970, 56 Rue Leblanc, 75015 Paris, France
| | - Zafrul Hasan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Ilaria Del Gaudio
- Université Paris Cité, PARCC, INSERM U970, 56 Rue Leblanc, 75015 Paris, France
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Eric Camerer
- Université Paris Cité, PARCC, INSERM U970, 56 Rue Leblanc, 75015 Paris, France
| | - Long N Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore; Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore; Cardiovascular Disease Research (CVD) Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; Immunology Program, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore; Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore.
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12
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Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites 2022; 12:metabo12070584. [PMID: 35888710 PMCID: PMC9319858 DOI: 10.3390/metabo12070584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.
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Affiliation(s)
- Nils Hoffmann
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), 52425 Jülich, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
| | - Gerhard Mayer
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany;
| | - Canan Has
- Biological Mass Spectrometry, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;
- University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- CENTOGENE GmbH, 18055 Rostock, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Fadi Al Machot
- Faculty of Science and Technology, Norwegian University for Life Science (NMBU), 1433 Ås, Norway;
| | - Dominik Schwudke
- Bioanalytical Chemistry, Forschungszentrum Borstel, Leibniz Lung Center, 23845 Borstel, Germany;
- Airway Research Center North, German Center for Lung Research (DZL), 23845 Borstel, Germany
- German Center for Infection Research (DZIF), TTU Tuberculosis, 23845 Borstel, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Katrin Marcus
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
| | - Martin Eisenacher
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, 85764 Neuherberg, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
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13
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Validation of a multiplexed and targeted lipidomics assay for accurate quantification of lipidomes. J Lipid Res 2022; 63:100218. [PMID: 35489416 PMCID: PMC9168725 DOI: 10.1016/j.jlr.2022.100218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022] Open
Abstract
A major challenge of lipidomics is to determine and quantify the precise content of complex lipidomes to the exact lipid molecular species. Often, multiple methods are needed to achieve sufficient lipidomic coverage to make these determinations. Multiplexed targeted assays offer a practical alternative to enable quantitative lipidomics amenable to quality control standards within a scalable platform. Herein, we developed a multiplexed normal phase liquid chromatography-hydrophilic interaction chromatography multiple reaction monitoring method that quantifies lipid molecular species across over 20 lipid classes spanning wide polarities in a single 20-min run. Analytical challenges such as in-source fragmentation, isomer separations, and concentration dynamics were addressed to ensure confidence in selectivity, quantification, and reproducibility. Utilizing multiple MS/MS product ions per lipid species not only improved the confidence of lipid identification but also enabled the determination of relative abundances of positional isomers in samples. Lipid class-based calibration curves were applied to interpolate lipid concentrations and guide sample dilution. Analytical validation was performed following FDA Bioanalytical Method Validation Guidance for Industry. We report repeatable and robust quantitation of 900 lipid species measured in NIST-SRM-1950 plasma, with over 700 lipids achieving inter-assay variability below 25%. To demonstrate proof of concept for biomarker discovery, we analyzed plasma from mice treated with a glucosylceramide synthase inhibitor, benzoxazole 1. We observed expected reductions in glucosylceramide levels in treated animals but, more notably, identified novel lipid biomarker candidates from the plasma lipidome. These data highlight the utility of this qualified lipidomic platform for enabling biological discovery.
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14
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TRACES: A Lightweight Browser for Liquid Chromatography-Multiple Reaction Monitoring-Mass Spectrometry Chromatograms. Metabolites 2022; 12:metabo12040354. [PMID: 35448541 PMCID: PMC9027295 DOI: 10.3390/metabo12040354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/28/2022] Open
Abstract
In targeted metabolomic analysis using liquid chromatography–multiple reaction monitoring–mass spectrometry (LC-MRM-MS), hundreds of MRMs are performed in a single run, yielding a large dataset containing thousands of chromatographic peaks. Automation tools for processing large MRM datasets have been reported, but a visual review of chromatograms is still critical, as real samples with biological matrices often cause complex chromatographic patterns owing to non-specific, insufficiently separated, isomeric, and isotopic components. Herein, we report the development of new software, TRACES, a lightweight chromatogram browser for MRM-based targeted LC-MS analysis. TRACES provides rapid access to all MRM chromatograms in a dataset, allowing users to start ad hoc data browsing without preparations such as loading compound libraries. As a special function of the software, we implemented a chromatogram-level deisotoping function that facilitates the identification of regions potentially affected by isotopic signals. Using MRM libraries containing precursor and product formulae, the algorithm reveals all possible isotopic interferences in the dataset and generates deisotoped chromatograms. To validate the deisotoping function in real applications, we analyzed mouse tissue phospholipids in which isotopic interference by molecules with different fatty-acyl unsaturation levels is known. TRACES successfully removed isotopic signals within the MRM chromatograms, helping users avoid inappropriate regions for integration.
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15
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Serum Lipidome Signatures of Dogs with Different Endocrinopathies Associated with Hyperlipidemia. Metabolites 2022; 12:metabo12040306. [PMID: 35448493 PMCID: PMC9031822 DOI: 10.3390/metabo12040306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/01/2022] Open
Abstract
Hyperlipidemia (hypertriglyceridemia, hypercholesterolemia) is a common finding in human and veterinary patients with endocrinopathies (e.g., hypothyroidism and hypercortisolism (Cushing’s syndrome; CS)). Despite emerging use of lipidomics technology in medicine, the lipid profiles of these endocrinopathies have not been evaluated and characterized in dogs. The aim of this study was to compare the serum lipidomes of dogs with naturally occurring CS or hypothyroidism with those of healthy dogs. Serum samples from 39 dogs with CS, 45 dogs with hypothyroidism, and 10 healthy beagle dogs were analyzed using a targeted lipidomics approach with liquid chromatography-mass spectrometry. There were significant differences between the lipidomes of dogs with CS, hypothyroidism, and the healthy dogs. The most significant changes were found in the lysophosphatidylcholines, lysophosphatidylethanolamines, lysophosphatidylinositols, phosphatidylcholines, phosphatidylethanolamines, phosphatidylglycerols, ceramides, and sphingosine 1-phosphates. Lipid alterations were especially pronounced in dogs with hypothyroidism. Several changes suggested a more atherogenic lipid profile in dogs with HT than in dogs with CS. In this study, we found so far unknown effects of naturally occurring hypothyroidism and CS on lipid metabolism in dogs. Our findings provide starting points to further examine differences in occurrence of atherosclerotic lesion formation between the two diseases.
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16
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Si-Hung L, Bamba T. Current state and future perspectives of supercritical fluid chromatography. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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17
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Ghorasaini M, Mohammed Y, Adamski J, Bettcher L, Bowden JA, Cabruja M, Contrepois K, Ellenberger M, Gajera B, Haid M, Hornburg D, Hunter C, Jones CM, Klein T, Mayboroda O, Mirzaian M, Moaddel R, Ferrucci L, Lovett J, Nazir K, Pearson M, Ubhi BK, Raftery D, Riols F, Sayers R, Sijbrands EJG, Snyder MP, Su B, Velagapudi V, Williams KJ, de Rijke YB, Giera M. Cross-Laboratory Standardization of Preclinical Lipidomics Using Differential Mobility Spectrometry and Multiple Reaction Monitoring. Anal Chem 2021; 93:16369-16378. [PMID: 34859676 PMCID: PMC8674878 DOI: 10.1021/acs.analchem.1c02826] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022]
Abstract
Modern biomarker and translational research as well as personalized health care studies rely heavily on powerful omics' technologies, including metabolomics and lipidomics. However, to translate metabolomics and lipidomics discoveries into a high-throughput clinical setting, standardization is of utmost importance. Here, we compared and benchmarked a quantitative lipidomics platform. The employed Lipidyzer platform is based on lipid class separation by means of differential mobility spectrometry with subsequent multiple reaction monitoring. Quantitation is achieved by the use of 54 deuterated internal standards and an automated informatics approach. We investigated the platform performance across nine laboratories using NIST SRM 1950-Metabolites in Frozen Human Plasma, and three NIST Candidate Reference Materials 8231-Frozen Human Plasma Suite for Metabolomics (high triglyceride, diabetic, and African-American plasma). In addition, we comparatively analyzed 59 plasma samples from individuals with familial hypercholesterolemia from a clinical cohort study. We provide evidence that the more practical methyl-tert-butyl ether extraction outperforms the classic Bligh and Dyer approach and compare our results with two previously published ring trials. In summary, we present standardized lipidomics protocols, allowing for the highly reproducible analysis of several hundred human plasma lipids, and present detailed molecular information for potentially disease relevant and ethnicity-related materials.
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Affiliation(s)
- Mohan Ghorasaini
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands
- Genome
BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Jerzy Adamski
- Institute
of Experimental Genetics, German Research Center for Environmental
Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Institute
of Biochemistry, Faculty of Medicine, University
of Ljubljana, Vrazov
Trg 2, Ljubljana 1000, Slovenia
| | - Lisa Bettcher
- Northwest
Metabolomics Research Center, Department of Anesthesiology, University of Washington, Seattle, Washington 98109, United States
| | - John A. Bowden
- Department
of Physiological Sciences, College of Veterinary Medicine, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Matias Cabruja
- Department
of Genetics, School of Medicine, Stanford
University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Kévin Contrepois
- Department
of Genetics, School of Medicine, Stanford
University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Mathew Ellenberger
- Department
of Genetics, School of Medicine, Stanford
University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Bharat Gajera
- Metabolomics
Unit, Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, Biomedicum 2U, Helsinki 00014, Finland
| | - Mark Haid
- Metabolomics
and Proteomics Core, German Research Center for Environmental Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - Daniel Hornburg
- Department
of Genetics, School of Medicine, Stanford
University, 300 Pasteur Drive, Stanford, California 94305, United States
| | | | - Christina M. Jones
- Material Measurement Laboratory, National
Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Theo Klein
- Department
of Clinical Chemistry, University Medical Center, Erasmus MC, Rotterdam, 3000CA, The Netherlands
| | - Oleg Mayboroda
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands
| | - Mina Mirzaian
- Department
of Clinical Chemistry, University Medical Center, Erasmus MC, Rotterdam, 3000CA, The Netherlands
| | - Ruin Moaddel
- National Institute on Aging, National Institutes of
Health, Baltimore, Maryland 21224, United
States
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of
Health, Baltimore, Maryland 21224, United
States
| | - Jacqueline Lovett
- National Institute on Aging, National Institutes of
Health, Baltimore, Maryland 21224, United
States
| | - Kenneth Nazir
- Metabolomics
Unit, Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, Biomedicum 2U, Helsinki 00014, Finland
| | | | | | - Daniel Raftery
- Northwest
Metabolomics Research Center, Department of Anesthesiology, University of Washington, Seattle, Washington 98109, United States
| | - Fabien Riols
- Metabolomics
and Proteomics Core, German Research Center for Environmental Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | | | - Eric J. G. Sijbrands
- Department of Internal Medicine, University
Medical Center, Erasmus MC, Rotterdam 3000CA, The Netherlands
| | - Michael P. Snyder
- Department
of Genetics, School of Medicine, Stanford
University, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Baolong Su
- Department of Biological
Chemistry, University
of California, Los Angeles, California 90095, United States
| | - Vidya Velagapudi
- Metabolomics
Unit, Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, Biomedicum 2U, Helsinki 00014, Finland
| | - Kevin J. Williams
- Department of Biological
Chemistry, University
of California, Los Angeles, California 90095, United States
| | - Yolanda B. de Rijke
- Department
of Clinical Chemistry, University Medical Center, Erasmus MC, Rotterdam, 3000CA, The Netherlands
| | - Martin Giera
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, Leiden 2333ZA, The Netherlands
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18
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Ho WY, Chang JC, Lim K, Cazenave-Gassiot A, Nguyen AT, Foo JC, Muralidharan S, Viera-Ortiz A, Ong SJM, Hor JH, Agrawal I, Hoon S, Arogundade OA, Rodriguez MJ, Lim SM, Kim SH, Ravits J, Ng SY, Wenk MR, Lee EB, Tucker-Kellogg G, Ling SC. TDP-43 mediates SREBF2-regulated gene expression required for oligodendrocyte myelination. J Cell Biol 2021; 220:212536. [PMID: 34347016 PMCID: PMC8348376 DOI: 10.1083/jcb.201910213] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/16/2020] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
Cholesterol metabolism operates autonomously within the central nervous system (CNS), where the majority of cholesterol resides in myelin. We demonstrate that TDP-43, the pathological signature protein for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), influences cholesterol metabolism in oligodendrocytes. TDP-43 binds directly to mRNA of SREBF2, the master transcription regulator for cholesterol metabolism, and multiple mRNAs encoding proteins responsible for cholesterol biosynthesis and uptake, including HMGCR, HMGCS1, and LDLR. TDP-43 depletion leads to reduced SREBF2 and LDLR expression, and cholesterol levels in vitro and in vivo. TDP-43-mediated changes in cholesterol levels can be restored by reintroducing SREBF2 or LDLR. Additionally, cholesterol supplementation rescues demyelination caused by TDP-43 deletion. Furthermore, oligodendrocytes harboring TDP-43 pathology from FTD patients show reduced HMGCR and HMGCS1, and coaggregation of LDLR and TDP-43. Collectively, our results indicate that TDP-43 plays a role in cholesterol homeostasis in oligodendrocytes, and cholesterol dysmetabolism may be implicated in TDP-43 proteinopathies-related diseases.
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Affiliation(s)
- Wan Yun Ho
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jer-Cherng Chang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kenneth Lim
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Computational Biology Programme, Faculty of Science, National University of Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- 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
| | - Aivi T Nguyen
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Juat Chin Foo
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Sneha Muralidharan
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Ashley Viera-Ortiz
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sarah J M Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jin Hui Hor
- Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore
| | - Ira Agrawal
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shawn Hoon
- Molecular Engineering Laboratory, A*STAR Research Entities, Singapore
| | | | - Maria J Rodriguez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Su Min Lim
- Department of Neurology, and Biomedical Research Institute, Hanyang University College of Medicine, Seoul, South Korea.,Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Seung Hyun Kim
- Department of Neurology, and Biomedical Research Institute, Hanyang University College of Medicine, Seoul, South Korea
| | - John Ravits
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Shi-Yan Ng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, A*STAR Research Entities, 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
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Greg Tucker-Kellogg
- Computational Biology Programme, Faculty of Science, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Shuo-Chien Ling
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Program in Neuroscience and Behavior Disorders, Duke-National University of Singapore Medical School, Singapore
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