Pushing the boundaries: How Pierre Sabatier is helping to show that protein turnover can be studied in individual cells

Pierre Sabatier, a proteomics researcher working at Uppsala University with Prof. Karl-Henrik Grinnemo as well as in Jesper Velgaard Olsen 's lab at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen , is demonstrating that protein turnover can be studied in individual cells. Beyond proteomics, he’s also contributing to research on?metabolic diseases, which has recently seen rapid advances.

From genomics to proteomics: a transformative journey

Pierre's path to proteomics was shaped by inspiring mentors. "I owe my interest in proteomics to the amazing teachers of the MSc program in Lille, particularly Prof. Michel Salzet and Prof. Isabelle Fournier," he recalls. Their engaging teaching style and hands-on approach not only sparked Pierre's curiosity, but also guided his career path. "I am still not sure whether I liked proteomics from the start or if it was their teaching style which was really appealing to me - surely a bit of both!"

His experience in Lille marked a significant shift in Pierre's focus from genomics to proteomics. The decision has proven fruitful, as Pierre reflects, "I have not considered pursuing anything else since, and I am still having a lot of fun at work."

The single-cell revolution

Pierre's research journey led him to the Karolinska Institutet for his PhD studies under Prof. Roman Zubarev. It was here that a pivotal moment occurred - one that would shape the trajectory of his career.

"It was when I learned that single-cell proteomics analysis was possible," Pierre remembers vividly. "We were still located in the old building at Karolinska Institutet at the time. This was early on in my PhD studies - I did not have extensive experience in proteomics yet, so it sounded even more fascinating."

This revelation opened up a world of possibilities, making Pierre reconsider what was achievable in the field. This led him to pursue his postdoc in Prof. Jesper Olsen's lab at the University of Copenhagen. There, he met Dr. Zilu Ye, who was actively developing single-cell proteomics (SCP) workflows. "Zilu is very hardworking, focused and forward-thinking, so I got completely caught up in the crazy momentum of the field," Pierre reflected. "I literally put my other projects on hold to focus on the multiple single cell projects we developed since then. I truly enjoy method and technology development, and SCP is pushing the boundaries of what is possible in proteomics. It also offers tremendous opportunities in biology and medicine that would not be possible with bulk analysis.”

Pushing the boundaries: the pulsed SILAC breakthrough

One of the more memorable experiences of Pierre's career came during his time in Jesper's lab - the development of pulsed SILAC at the single-cell level. This breakthrough allowed for the study of protein turnover in individual cells.

“This was exciting because it provided sufficient depth for envisioning large-scale biological studies. The main highlight is that we showed that measurements of relative turnover is possible in single cells," he explains. "We applied this method to study the dynamics of protein turnover during the differentiation of stem cells over two months."

This project was not without its challenges. Pierre had to coordinate the stem cell differentiation process with precise sampling times, ensuring every component of the workflow performed flawlessly for two months straight, since they couldn’t restart or wait once the differentiation had begun. This left very little margin for potential technical issues.

"It was quite a bit of pressure," he admits. "I started planning as soon as I was back from Christmas holidays. I took a lot of precautions for the cells and had many back-ups to ensure that everything goes smoothly." This was especially important for Pierre due to the risk of bacterial contamination, since he doesn’t grow the stem cells with antibiotics.

As if that wasn’t enough pressure, significant resources were invested into the latest technological advancements for the project. Being able to measure to a satisfyingly accurate level required the most advanced tools - tools like Thermo’s Orbitrap Astral instrument, the Evosep One LC, and increasingly more sensitive chromatography from IonOpticks’ Aurora Series range. "That's the first time in my career that I felt like I absolutely needed to make it happen, or it would be such a huge waste of resources," Pierre reflects.

Despite these and further challenges, including some broken piezo dispending capillaries on the cellenONE, the project went fairly smoothly. The extensive preparation had paid off, and the project's success demonstrated that SCP workflows have become robust and reliable enough for such complex studies.

“Before IonOpticks’ columns, the analytical depth we are currently achieving would have been difficult to reach in single-cell proteomics and in phosphoproteomics analysis with very limited sample amounts. The pulsed SILAC analysis would have been even more challenging since we needed every bit of sensitivity because the single-cell signal is divided.” The reproducibility and improved analytical depth of Aurora Series columns are key to the sensitive workflows Pierre uses.

Find the full study here.

Beyond proteomics: stem cells and metabolic diseases

While single-cell proteomics remains at the core of Pierre's work, his research interests have expanded to include stem cell-derived models, diabetes and obesity. His fascination with stem cells began during his time in Prof. Zubarev’s lab, working with Assoc. Prof. Sergey Rodin.

"I always found fascinating the idea that one could, in theory, recreate any organ from one cell type that can be grown in culture, and even further, from reprogrammed patient cells to perform autologous transplantation," Pierre explains. “3D organoid models provide a balance between traditional 2D cell cultures and animal models, enhancing biological relevance, particularly for pre-clinical studies.”

His more recent focus on diabetes and obesity developed through collaborations with researchers in the field. "Due to the growing prevalence of metabolic diseases and the development of new therapies such as GLP-1R agonists, research in diabetes and obesity has seen rapid advances much like SCP," Pierre notes. "This has created exciting opportunities for collaboration and development."

Looking to the future

As Pierre continues his work at the Department of Surgical Sciences at Uppsala University with Prof. Karl-Henrik Grinnemo, he remains excited about the future of proteomics. "I am looking forward to all the exciting developments in proteomics that will likely come out in the coming years! The field is evolving fast, which really keeps me motivated and engaged with a constant flow of new opportunities.”

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