Deciphering lipid structures based on platform-independent decision rules

Hartler, Jürgen; Triebl, Alexander; Ziegl, Andreas; Trötzmüller, Martin; Rechberger, Gerald; Zeleznik, Oana A.; Zierler, Kathrin A.; Torta, Federico; Cazenave-Gassiot, Amaury; Wenk, Markus R.; Fauland, Alexander; Wheelock, Craig E.; Armando, Aaron M.; Quehenberger, Oswald; Zhang, Qifeng; Wakelam, Michael J.O.; Haemmerle, Guenter; Spener, Friedrich; Köfeler, Harald; Thallinger, Gerhard G.

doi:10.1038/nmeth.4470

Cited by 126 publications

(128 citation statements)

References 26 publications

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“…This will include comprehensive genomic analysis focusing on small RNA species as initiated previously in a study for monitoring the immunomodulatory potential of neonatal umbilical cord stromal cell-derived EVs [18]. Our quantitative EV purification approach will also allow for combining lipidomics, glycomics and metabolomics for a more broad view on PLX-EV biology using upcoming technology [35]- [37]. EV characterization can not be limited to key pathways of angiogenesis and immunity.…”

Section: Discussionmentioning

confidence: 99%

A functional corona around extracellular vesicles enhances angiogenesis during skin regeneration and signals in immune cells

Wolf

Poupardin

Ebner-Peking

et al. 2019

Preprint

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words)Allogeneic regenerative cell therapy has shown surprising results despite lack of engraftment of the transplanted cells. Their efficacy was so far considered to be mostly due to secreted trophic factors. We hypothesized that extracellular vesicles (EVs) can also contribute to their mode of action. Here we provide evidence that EVs derived from therapeutic placental-expanded (PLX) stromal cells are potent inducers of angiogenesis and modulate immune cell proliferation in a dose-dependent manner.Crude EVs were enriched >100-fold from large volume PLX conditioned media via tangential flow filtration (TFF) as determined by tunable resistive pulse sensing (TRPS).Additional TFF purification was devised to separate EVs from cell-secreted soluble factors. EV identity was confirmed by western blot, calcein-based flow cytometry and electron microscopy. Surface marker profiling of tetraspanin-positive EVs identified expression of cell-and matrix-interacting adhesion molecules. Differential tandem mass tag proteomics comparing PLX-EVs to PLX-derived soluble factors revealed significant differential enrichment of 258 proteins in purified PLX-EVs involved in angiogenesis, cell movement and immune system signaling. At the functional level, PLX-EVs and cells inhibited T cell mitogenesis. PLX-EVs and soluble factors displayed dose-dependent proangiogenic potential by enhancing tube-like structure formation in vitro.Our findings indicate that the mode of PLX action involves an EV-mediated proangiogenic function and immune response modulation that may help explaining clinical efficacy beyond presence of the transplanted allogeneic cells.

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Section: Discussionmentioning

confidence: 99%

A functional corona around extracellular vesicles enhances angiogenesis during skin regeneration and signals in immune cells

Wolf

Poupardin

Ebner-Peking

et al. 2019

Preprint

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“…From the Fourier transform mass spectrometry preview scan, the 10 most abundant m/z values were picked in data-dependent acquisition mode, fragmented in the linear ion trap analyzer, and ejected at nominal mass resolution. Normalized collision energy was set to 50%, the repeat count was 2, and the exclusion duration was set at 10 s. Data analysis was performed using Lipid Data Analyzer, a custom-developed software tool (60,61).…”

Section: Crystallizationmentioning

confidence: 99%

Inward-facing conformation of a multidrug resistance MATE family transporter

Zakrzewska

Mehdipour

Malviya

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Multidrug and toxic compound extrusion (MATE) transporters mediate excretion of xenobiotics and toxic metabolites, thereby conferring multidrug resistance in bacterial pathogens and cancer cells. Structural information on the alternate conformational states and knowledge of the detailed mechanism of MATE transport are of great importance for drug development. However, the structures of MATE transporters are only known in V-shaped outward-facing conformations. Here, we present the crystal structure of a MATE transporter from Pyrococcus furiosus (PfMATE) in the long-soughtafter inward-facing state, which was obtained after crystallization in the presence of native lipids. Transition from the outward-facing state to the inward-facing state involves rigid body movements of transmembrane helices (TMs) 2-6 and 8-12 to form an inverted V, facilitated by a loose binding of TM1 and TM7 to their respective bundles and their conformational flexibility. The inward-facing structure of PfMATE in combination with the outward-facing one supports an alternating access mechanism for the MATE family transporters. multidrug resistance | membrane protein structure | MATE transporter | inward-facing conformation | lipids

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“…20,21 The metabolites were generally identified by the matching of mass spectra and fragment ions with high accuracy to theoretical values in a database and matching of the retention times of the chromatogram to chemical standards, 22,23 which defined the quality of identification. 24,25 However, there were still isomeric and isobaric species, such as lipids. High-definition mass spectrometry (HDMS) is a technology that relies on the mobility of ions, including small molecules, according to the charge, shape, and size in the gas phase inside the MS instrument.…”

Section: Metabolomics Is Classified Into Targeted Metabolomics (T-met)mentioning

confidence: 99%

“…The metabolites were generally identified by the matching of mass spectra and fragment ions with high accuracy to theoretical values in a database and matching of the retention times of the chromatogram to chemical standards, which defined the quality of identification . However, there were still isomeric and isobaric species, such as lipids.…”

Section: Introductionmentioning

confidence: 99%

Identification of novel biomarkers of hepatocellular carcinoma by high‐definition mass spectrometry: Ultrahigh‐performance liquid chromatography quadrupole time‐of‐flight mass spectrometry and desorption electrospray ionization mass spectrometry imaging

Nagai

Uranbileg

Chen

et al. 2019

Rapid Comm Mass Spectrometry

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Rationale Hepatocellular carcinoma (HCC) is a highly malignant disease for which the development of prospective or prognostic biomarkers is urgently required. Although metabolomics is widely used for biomarker discovery, there are some bottlenecks regarding the comprehensiveness of detected features, reproducibility of methods, and identification of metabolites. In addition, information on localization of metabolites in tumor tissue is needed for functional analysis. Here, we developed a wide‐polarity global metabolomics (G‐Met) method, identified HCC biomarkers in human liver samples by high‐definition mass spectrometry (HDMS), and demonstrated localization in cryosections using desorption electrospray ionization MS imaging (DESI‐MSI) analysis. Methods Metabolic profiling of tumor (n = 38) and nontumor (n = 72) regions in human livers of HCC was performed by an ultrahigh‐performance liquid chromatography quadrupole time‐of‐flight MS (UHPLC/QTOFMS) instrument equipped with a mixed‐mode column. The HCC biomarker candidates were extracted by multivariate analyses and identified by matching values of the collision cross section and their fragment ions on the mass spectra obtained by HDMS. Cryosections of HCC livers, which included both tumor and nontumor regions, were analyzed by DESI‐MSI. Results From the multivariate analysis, m/z 904.83 and m/z 874.79 were significantly high and low, respectively, in tumor samples and were identified as triglyceride (TG) 16:0/18:1(9Z)/20:1(11Z) and TG 16:0/18:1(9Z)/18:2(9Z,12Z) using the synthetic compounds. The TGs were clearly localized in the tumor or nontumor areas of the cryosection. Conclusions Novel biomarkers for HCC were identified by a comprehensive and reproducible G‐Met method with HDMS using a mixed‐mode column. The combination analysis of UHPLC/QTOFMS and DESI‐MSI revealed that the different molecular species of TGs were associated with tumor distribution and were useful for characterizing the progression of tumor cells and discovering prospective biomarkers.

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Deciphering lipid structures based on platform-independent decision rules

Cited by 126 publications

References 26 publications

A functional corona around extracellular vesicles enhances angiogenesis during skin regeneration and signals in immune cells

A functional corona around extracellular vesicles enhances angiogenesis during skin regeneration and signals in immune cells

Inward-facing conformation of a multidrug resistance MATE family transporter

Identification of novel biomarkers of hepatocellular carcinoma by high‐definition mass spectrometry: Ultrahigh‐performance liquid chromatography quadrupole time‐of‐flight mass spectrometry and desorption electrospray ionization mass spectrometry imaging

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