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MassSpec-Forum2024: Workshop – Lipidomics-LIFS Bioinformatics Training

The MassSpec-Forum Vienna 2024 kicked off on Wednesday, February 21st, with a morning dedicated to insightful workshops. 

The Workshop 3 on Lipidomics-LIFS Bioinformatics Training, was conducted by Dominik Kopczynski, Nils Hoffmann, and Robert Ahrends from the University of Vienna. The session, held in parallel with other workshops, focused on the intricacies of lipidomics and the application of bioinformatics tools, specifically utilizing the Lipidomics-LIFS platform. Attendees delved into advanced techniques and methodologies, gaining hands-on experience in deciphering lipid data.

This workshop not only provided a unique learning opportunity, but also showcased the commitment of MassSpec-Forum Vienna 2024 to cover diverse aspects of mass spectrometry, ensuring participants received a comprehensive education in this dynamic field. The event’s emphasis on practical training and engagement set a tone for the subsequent days of the conference.

Photos by David Loibnegger and Claude Molitor

68th Annual GTH Meeting 2024

The 68th Annual Meeting of the GTH 2024 took place from February 27 to March 01 in Vienna under the theme “Building Bridges in Coagulation.”

The conference venue was the Hofburg, beautifully arranged for the occasion. The central focus of the conference was on thrombosis and hemostasis (GTH).

The talks featured a combination of invited international speakers, primarily doctors engaged in research presenting study results and updates on ongoing research, and young researchers, mainly PhDs in the medical field aspiring to become doctors. Also Bianca de Jonckheere, the PhD in the working group Lipidomics at the University of Vienna, presented her Megakaryocytes Project. Additionally, there were symposia from industry partners interspersed throughout the conference.

During breaks, attendees could enjoy snacks and coffee in the Vendor Hall, where a noticeable emphasis on sustainability was observed. Recyclable materials were used. The networking dinner kicked off with a champagne reception, followed by a one-hour exploration of the Weltmuseum and concluded with a meal accompanied by a dance performance reminiscent of a classical Viennese ball.

Pic by Robert Ahrends

LipidSpace LIFS Tool

LipidSpace is a stand-alone tool to analyze and compare lipidomes by assessing their structural differences.

A graph-based comparison of lipid structures that allows to calculate distances between lipids and to determine similarities across lipidomes. It allows for a rapid (re)analysis of experiments, identifies lipids responsible for shaping the respective lipidome, and provides methods for quality control.

LipidSpace has been built and tested under Windows 10 and Ubuntu 22.04 Linux. It comes with four built-in tutorials to get you started.

More: https://lifs-tools.org/lipidspace.html

Accurate Sphingolipid Quantification Reducing Fragmentation Bias by Nonlinear Models

Accurate quantification of molecular sphingolipid species is essential for a comprehensive understanding of their diverse roles in physiological and pathological contexts. The conventional method of quantifying sphingolipids, which relies on sphingoid base-derived fragments relative to a class-specific internal standard, often falls short in addressing the structural diversity of these bioactive molecules. To overcome this limitation, we have developed a novel fragmentation model to correct for structural differences, providing a solution that transcends the constraints of the traditional “one standard per class” strategy. Notably, our approach is independent of the internal standard, instrumental setup, and collision energy. Furthermore, we have integrated this correction method into a user-friendly KNIME workflow. Validation results affirm the efficacy of our approach in accurately quantifying ceramide subclasses across diverse biological matrices. This advancement opens new horizons for exploring sphingolipid metabolism, offering profound insights into its implications.

Go to the publication here.

Decoding Blood Platelet Production: The Intricate Role of Lipids

Scientists unveiled a deeper understanding of megakaryocyte differentiation and blood platelet production, a process crucial for maintaining healthy blood clotting and preventing excessive bleeding. The study featured in “Nature Cardiovascular Research,” led by chemist Robert Ahrends from the University of Vienna and cardiologist Oliver Borst from the University of Tübingen, sheds light on the intricate role of lipids – the building blocks of cell membranes – in the formation of these vital blood components.

Blood platelets, tiny disk-shaped cells in our bloodstream, play a pivotal role in wound healing and preventing excessive bleeding. The process by which these platelets are produced, known as thrombopoiesis, begins with the differentiation of specialized cells called megakaryocytes. These megakaryocytes undergo a series of transformations, ultimately giving rise to thousands of blood platelets.

“It is astonishing that despite its clinical importance, neither a quantitative lipid inventory nor a map of the lipid metabolism of megakaryocytes has been available,” says Robert Ahrends.

So far, the study of megakaryocyte differentiation and platelet production has centered on enzymes related only to sphingolipid metabolism, but until now, the exact nature of the lipid species involved, as well as their metabolizing enzymes and their impact on the process, remained largely unknown. Using advanced mass spectrometry-based multiomics, the research team investigated the mechanisms of lipidome modulation of megakaryocytes as they matured and formed platelets.

Shaping anionic membranes: A lipid-driven transformation

As the megakaryocytes differentiated, they underwent substantial changes in lipid membrane composition, resulting in what the team termed an “anionic membrane phenotype.” This shift was found to be directly linked to the regulation of crucial proteins and kinases involved in platelet formation.

The study also highlighted the role of fatty acids – the building blocks of lipids – in this process. The researchers found that the uptake of fatty acids increased significantly during megakaryocyte maturation, alongside a boost in fatty acid synthesis. Manipulation of such resulted in profound thrombocytopenia, a condition characterized by abnormally low platelet levels.

Importance for cardiovascular fitness

In essence, this study offers a remarkable new perspective on megakaryocyte differentiation and platelet production, highlighting the interplay between lipids and proteins on cellular membrane transformation. “Our study provides a foundation for exploring how disruptions in lipid metabolism, seen in conditions like obesity, might affect platelet production and overall cardiovascular health,” says cardiologist Oliver Borst. Beyond scientific insights, this discovery holds promise for new avenues in addressing health challenges on the horizon.

Fig. 1. Lipid driven functional regulation and underlying mechanisms of MK maturation and thrombopoiesis.

This study focuses on the functional analysis and regulation of MK maturation and proplatelet formation, utilizing a multiomics approach and incorporating both in vitro and in vivo methodologies. To develop the multiomics method, hematopoietic stem cells were isolated from murine BM and subjected to a 7-day differentiation protocol with TPO. The SIMPLEX workflow, enabling simultaneous lipid and protein sample preparation, was employed to comprehensively determine the general molecular composition of MKs. The results revealed significant anionic lipid membrane remodeling and relocalization of the CKIP-1/CK2α complex to the plasma membrane, which appear to be essential for adequate platelet biogenesis. The graphical illustration was generated using BioRender.

Go to the publication in Nature Cardiovascular Research

Scientific contact
Prof. Dr. Robert Ahrends
Institut für Analytische Chemie
Universität Wien
1090 – Wien, Währinger Straße 38
+43-1-4277-52304
robert.ahrends@univie.ac.at
https://lipidomics.at/

8th Lipidomics Forum & 2nd ILS Conference August 27th – 30th 2023

The 8th Lipidomics Forum and 2nd International Lipidomics Society (ILS) Conference convened from August 27th to 30th, 2023. It provided a dynamic platform for researchers, scientists, and industry experts to delve into the latest advancements in lipidomics.

The Local Organizing Committee, headed by Robert Ahrends and his working group at the University of Vienna, successfully planned and organized the event. The conference schedule was thoughtfully created to cover the diverse interests and expertise of the attendees. The four-day event commenced with a series of workshops and an opening by Vice-Rector Manuela Baccarini.

Keynote speakers from academia and industry delivered exciting talks on emerging trends and challenges in lipidomics, laying the foundation for the ensuing discussions. The LIFS and LipiTUM workshops unfolded over the subsequent days, covering a spectrum of topics ranging from lipid profiling technologies and methodologies to the functional roles of lipids in health and disease. Participants discussed mass spectrometry techniques, chromatographic approaches, and bioinformatics tools employed in lipidomics research.

The Forum and the Conference also provided a unique platform for early-career scientists and graduate students to present their research through dedicated sessions and poster presentations. This initiative put together the next generation of lipidomics researchers and promoted a collaborative spirit within the scientific community.

In addition to the scientific program, the conference facilitated networking opportunities, allowing participants to establish connections with peers, mentors, and industry representatives.

The conference concluded on August 30th, 2023, and left a lasting impact on the lipidomics community. The organizers thank all attendees and are grateful for the industry sponsorship, making this meeting a vibrant event. We are looking forward to welcoming you again from the 14th to the 17th of September in 2025.

Pics by Martin Schaier.

Latest methods in lipidomics; Extraction: Quo vadis?

I was thrilled to have Gerhard Liebisch from Regensburg and Denise Wolrab with us on sample extraction. Both exciting talks gave our students great detail about what can go wrong in sample extraction during lipidomics experiments.

Gerhard Liebisch, Institute of Clinical Chemistry, Regensburg, Germany

PD Dr. Gerhard Liebisch obtained his Ph.D. at the University of Regensburg. His research interests focus on the development of MS methods for the quantification of lipid species. For more than 20 years, these methods have been applied in large-scale clinical studies and basic research. https://lipidomics-regensburg.de/

 

Denise Wolrab, University of Pardubice, Czech Republic

Dr. Denise Wolrab is an analytical chemist focusing on separation science and the application for the analysis of biomolecules, mainly using supercritical fluid chromatography hyphenated to mass spectrometry. After her Ph.D. at the University of Vienna in 2017, she obtained a postdoc position at the University of Pardubice responsible for the method development and application of lipidomics for cancer screening, mainly using UHPSFC/MS. Since 2020, Denise Wolrab has been PI and Grant Project manager at the University of Pardubice, evaluating the applicability of UHPSFC/MS for the metabolomic analysis of clinical samples.