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Hohenwallner K, Lamp LM, Peng L, Nuske M, Hartler J, Reid GE, Rampler E. FAIMS Shotgun Lipidomics for Enhanced Class- and Charge-State Separation Complemented by Automated Ganglioside Annotation. Anal Chem 2024; 96. [PMID: 39028917 PMCID: PMC11295132 DOI: 10.1021/acs.analchem.4c01313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/20/2024] [Accepted: 07/12/2024] [Indexed: 07/21/2024]
Abstract
The analysis of gangliosides is extremely challenging, given their structural complexity, lack of reference standards, databases, and software solutions. Here, we introduce a fast 6 min high field asymmetric ion mobility spectrometry (FAIMS) shotgun lipidomics workflow, along with a dedicated software solution for ganglioside detection. By ramping FAIMS compensation voltages, ideal ranges for different ganglioside classes were obtained. FAIMS revealed both class- and charge-state separation behavior based on the glycan headgroup moiety. The number of sialic acids attached to the glycan moiety correlates positively with their preferred charge states, i.e., trisialylated gangliosides were mainly present as [M - 3H]3- ions, whereas [M - 4H]4- and [M - 5H]5- ions were observed for GQ1 and GP1. For data evaluation, we developed a shotgun/FAIMS extension for the open-source Lipid Data Analyzer (LDA), enabling automated annotation of gangliosides up to the molecular lipid species level. This extension utilized combined orthogonal fragmentation spectra from CID, HCD, and 213 nm UVPD ion activation methods and covers 29 ganglioside classes, including acetylated and fucosylated modifications. With our new workflow and software extension 117 unique gangliosides species were identified in porcine brain extracts. While conventional shotgun lipidomics favored the observation of singly charged ganglioside species, the utilization of FAIMS made multiply charged lipid species accessible, resulting in an increased number of detected species, primarily due to an improved signal-to-noise ratio arising from FAIMS charge state filtering. Therefore, this FAIMS-driven workflow, complemented by new software capabilities, offers a promising strategy for complex ganglioside and glycosphingolipid characterization in shotgun lipidomics.
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Affiliation(s)
- Katharina Hohenwallner
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Leonida M. Lamp
- Institute
of Pharmaceutical Sciences, University of
Graz, Graz 8010, Austria
| | - Liuyu Peng
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Madison Nuske
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jürgen Hartler
- Institute
of Pharmaceutical Sciences, University of
Graz, Graz 8010, Austria
- Field
of Excellence BioHealth, University of Graz, Graz 8010, Austria
| | - Gavin E. Reid
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Pharmacology, University
of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Evelyn Rampler
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
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2
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Schengrund CL. Sphingolipids: Less Enigmatic but Still Many Questions about the Role(s) of Ceramide in the Synthesis/Function of the Ganglioside Class of Glycosphingolipids. Int J Mol Sci 2024; 25:6312. [PMID: 38928016 PMCID: PMC11203820 DOI: 10.3390/ijms25126312] [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: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
While much has been learned about sphingolipids, originally named for their sphinx-like enigmatic properties, there are still many unanswered questions about the possible effect(s) of the composition of ceramide on the synthesis and/or behavior of a glycosphingolipid (GSL). Over time, studies of their ceramide component, the sphingoid base containing the lipid moiety of GSLs, were frequently distinct from those performed to ascertain the roles of the carbohydrate moieties. Due to the number of classes of GSLs that can be derived from ceramide, this review focuses on the possible role(s) of ceramide in the synthesis/function of just one GSL class, derived from glucosylceramide (Glc-Cer), namely sialylated ganglio derivatives, initially characterized and named gangliosides (GGs) due to their presence in ganglion cells. While much is known about their synthesis and function, much is still being learned. For example, it is only within the last 15-20 years or so that the mechanism by which the fatty acyl component of ceramide affected its transport to different sites in the Golgi, where it is used for the synthesis of Glu- or galactosyl-Cer (Gal-Cer) and more complex GSLs, was defined. Still to be fully addressed are questions such as (1) whether ceramide composition affects the transport of partially glycosylated GSLs to sites where their carbohydrate chain can be elongated or affects the activity of glycosyl transferases catalyzing that elongation; (2) what controls the differences seen in the ceramide composition of GGs that have identical carbohydrate compositions but vary in that of their ceramide and vice versa; (3) how alterations in ceramide composition affect the function of membrane GGs; and (4) how this knowledge might be applied to the development of therapies for treating diseases that correlate with abnormal expression of GGs. The availability of an updatable data bank of complete structures for individual classes of GSLs found in normal tissues as well as those associated with disease would facilitate research in this area.
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Affiliation(s)
- Cara-Lynne Schengrund
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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Sirén H. Research of saccharides and related biocomplexes: A review with recent techniques and applications. J Sep Sci 2024; 47:e2300668. [PMID: 38699940 DOI: 10.1002/jssc.202300668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 05/05/2024]
Abstract
Saccharides and biocompounds as saccharide (sugar) complexes have various roles and biological functions in living organisms due to modifications via nucleophilic substitution, polymerization, and complex formation reactions. Mostly, mono-, di-, oligo-, and polysaccharides are stabilized to inactive glycosides, which are formed in metabolic pathways. Natural saccharides are important in food and environmental monitoring. Glycosides with various functionalities are significant in clinical and medical research. Saccharides are often studied with the chromatographic methods of hydrophilic interaction liquid chromatography and anion exchange chromatograpy, but also with capillary electrophoresis and mass spectrometry with their on-line coupling systems. Sample preparation is important in the identification of saccharide compounds. The cases discussed here focus on bioscience, clinical, and food applications.
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Affiliation(s)
- Heli Sirén
- Chemicum Building, University of Helsinki, Helsinki, Finland
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Santilli F, Fabrizi J, Martellucci S, Santacroce C, Iorio E, Pisanu ME, Chirico M, Lancia L, Pulcini F, Manganelli V, Sorice M, Delle Monache S, Mattei V. Lipid rafts mediate multilineage differentiation of human dental pulp-derived stem cells (DPSCs). Front Cell Dev Biol 2023; 11:1274462. [PMID: 38020931 PMCID: PMC10665896 DOI: 10.3389/fcell.2023.1274462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Cell outer membranes contain glycosphingolipids and protein receptors, which are integrated into glycoprotein domains, known as lipid rafts, which are involved in a variety of cellular processes, including receptor-mediated signal transduction and cellular differentiation process. In this study, we analyzed the lipidic composition of human Dental Pulp-Derived Stem Cells (DPSCs), and the role of lipid rafts during the multilineage differentiation process. The relative quantification of lipid metabolites in the organic fraction of DPSCs, performed by Nuclear Magnetic Resonance (NMR) spectroscopy, showed that mono-unsaturated fatty acids (MUFAs) were the most representative species in the total pool of acyl chains, compared to polyunsatured fatty acids (PUFAs). In addition, the stimulation of DPSCs with different culture media induces a multilineage differentiation process, determining changes in the gangliosides pattern. To understand the functional role of lipid rafts during multilineage differentiation, DPSCs were pretreated with a typical lipid raft affecting agent (MβCD). Subsequently, DPSCs were inducted to differentiate into osteoblast, chondroblast and adipoblast cells with specific media. We observed that raft-affecting agent MβCD prevented AKT activation and the expression of lineage-specific mRNA such as OSX, PPARγ2, and SOX9 during multilineage differentiation. Moreover, this compound significantly prevented the tri-lineage differentiation induced by specific stimuli, indicating that lipid raft integrity is essential for DPSCs differentiation. These results suggest that lipid rafts alteration may affect the signaling pathway activated, preventing multilineage differentiation.
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Affiliation(s)
- Francesca Santilli
- Biomedicine and Advanced Technologies Rieti Center, “Sabina Universitas”, Rieti, Italy
| | - Jessica Fabrizi
- Biomedicine and Advanced Technologies Rieti Center, “Sabina Universitas”, Rieti, Italy
- Department of Experimental Medicine, “Sapienza” University of Rome, Rome, Italy
| | - Stefano Martellucci
- Biomedicine and Advanced Technologies Rieti Center, “Sabina Universitas”, Rieti, Italy
| | - Costantino Santacroce
- Biomedicine and Advanced Technologies Rieti Center, “Sabina Universitas”, Rieti, Italy
| | - Egidio Iorio
- High Resolution NMR Unit, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Elena Pisanu
- High Resolution NMR Unit, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Mattea Chirico
- High Resolution NMR Unit, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Loreto Lancia
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Fanny Pulcini
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Valeria Manganelli
- Department of Experimental Medicine, “Sapienza” University of Rome, Rome, Italy
| | - Maurizio Sorice
- Department of Experimental Medicine, “Sapienza” University of Rome, Rome, Italy
| | - Simona Delle Monache
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Vincenzo Mattei
- Dipartimento di Scienze della Vita, della Salute e delle Professioni Sanitarie, Link Campus University, Rome, Italy
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Novoseletskaya ES, Evdokimov PV, Efimenko AY. Extracellular matrix-induced signaling pathways in mesenchymal stem/stromal cells. Cell Commun Signal 2023; 21:244. [PMID: 37726815 PMCID: PMC10507829 DOI: 10.1186/s12964-023-01252-8] [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: 06/16/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
The extracellular matrix (ECM) is a crucial component of the stem cell microenvironment, or stem-cell niches, and contributes to the regulation of cell behavior and fate. Accumulating evidence indicates that different types of stem cells possess a large variety of molecules responsible for interactions with the ECM, mediating specific epigenetic rearrangements and corresponding changes in transcriptome profile. Signals from the ECM are crucial at all stages of ontogenesis, including embryonic and postnatal development, as well as tissue renewal and repair. The ECM could regulate stem cell transition from a quiescent state to readiness to perceive the signals of differentiation induction (competence) and the transition between different stages of differentiation (commitment). Currently, to unveil the complex networks of cellular signaling from the ECM, multiple approaches including screening methods, the analysis of the cell matrixome, and the creation of predictive networks of protein-protein interactions based on experimental data are used. In this review, we consider the existing evidence regarded the contribution of ECM-induced intracellular signaling pathways into the regulation of stem cell differentiation focusing on mesenchymal stem/stromal cells (MSCs) as well-studied type of postnatal stem cells totally depended on signals from ECM. Furthermore, we propose a system biology-based approach for the prediction of ECM-mediated signal transduction pathways in target cells. Video Abstract.
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Affiliation(s)
- Ekaterina Sergeevna Novoseletskaya
- Faculty of Biology, Dayun New Town, Shenzhen MSU-BIT University, 1 International University Park Road, Dayun New Town, Longgang District, Shenzhen, Guangdong Province, P. R. China.
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Lomonosov Ave., 27/10, 119991, Moscow, Russia.
| | - Pavel Vladimirovich Evdokimov
- Materials Science Department, Lomonosov Moscow State University, Leninskie Gory, 1, Building 73, 119991, Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, 1-3, Moscow, Russia
| | - Anastasia Yurievna Efimenko
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Lomonosov Ave., 27/10, 119991, Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, Lomonosov Ave., 27/1, 119991, Moscow, Russia
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Mattei V, Delle Monache S. 10th Anniversary of Biomedicines-Advances in Mesenchymal Stem Cells. Biomedicines 2023; 11:2183. [PMID: 37626680 PMCID: PMC10452608 DOI: 10.3390/biomedicines11082183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Mesenchymal stromal cells (MSCs) are non-specialized adult stem cells (ASCs), cells that reproduce to provide specific cytotypes [...].
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Affiliation(s)
- Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100 Rieti, Italy
| | - Simona Delle Monache
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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Santilli F, Fabrizi J, Pulcini F, Santacroce C, Sorice M, Delle Monache S, Mattei V. Gangliosides and Their Role in Multilineage Differentiation of Mesenchymal Stem Cells. Biomedicines 2022; 10:biomedicines10123112. [PMID: 36551867 PMCID: PMC9775755 DOI: 10.3390/biomedicines10123112] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/10/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
Gangliosides (GGs) are a glycolipid class present on Mesenchymal Stem Cells (MSCs) surfaces with a critical appearance role in stem cell differentiation, even though their mechanistic role in signaling and differentiation remains largely unknown. This review aims to carry out a critical analysis of the predictive role of gangliosides as specific markers of the cellular state of undifferentiated and differentiated MSCs, towards the osteogenic, chondrogenic, neurogenic, and adipogenic lineage. For this reason, we analyzed the role of GGs during multilineage differentiation processes of several types of MSCs such as Umbilical Cord-derived MSCs (UC-MSCs), Bone Marrow-derived MSCs (BM-MSCs), Dental Pulp derived MSCs (DPSCs), and Adipose derived MSCs (ADSCs). Moreover, we examined the possible role of GGs as specific cell surface markers to identify or isolate specific stem cell isotypes and their potential use as additional markers for quality control of cell-based therapies.
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Affiliation(s)
- Francesca Santilli
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, Angelo Maria Ricci 35A, 02100 Rieti, Italy
| | - Jessica Fabrizi
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, Angelo Maria Ricci 35A, 02100 Rieti, Italy
- Department of Experimental Medicine, Sapienza University, Regina Elena 324, 00161 Rome, Italy
| | - Fanny Pulcini
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Vetoio, 67100 L’Aquila, Italy
| | - Costantino Santacroce
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, Angelo Maria Ricci 35A, 02100 Rieti, Italy
| | - Maurizio Sorice
- Department of Experimental Medicine, Sapienza University, Regina Elena 324, 00161 Rome, Italy
| | - Simona Delle Monache
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Vetoio, 67100 L’Aquila, Italy
- Correspondence: (S.D.M.); (V.M.)
| | - Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, Angelo Maria Ricci 35A, 02100 Rieti, Italy
- Correspondence: (S.D.M.); (V.M.)
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