Deciphering Progression Mechanisms in Chronic Kidney Disease With Single-Nucleus and Spatial Transcriptomics

Dr. Eric Feraille from the University of Geneva shares his thoughts on outsourcing bioinformatics and his experience using Genevia Technologies’ services. His group, which studies renal physiology and pathophysiology, contracted Genevia’s team for spatial transcriptomic and single-nucleus RNA-Seq data analysis.


Dr. Eric Feraille is a full professor of basic medicine at the University of Geneva. He leads the Laboratory of Physiology and Pathophysiology of Kidney Cells, focusing on the mechanisms of the progression of chronic kidney disease. The collaboration with Genevia Technologies began a year ago when the Feraille group started setting up single-nucleus RNA-Seq and spatial transcriptomic experiments. While the group had experience using omics approaches, mainly microarrays, these techniques were unfamiliar, and the institution lacked internal bioinformatics support.

– We study the role of corticoid metabolism in the progression of chronic kidney disease. The disease's progression may depend on the generation of cortisol; specifically, we focus on the role of an enzyme that metabolizes inactive glucocorticoids into an active form. We used Genevia's services to perform single-nucleus RNA-Seq data analysis to identify cell types involved in this process and to localize the kidney region where it occurs using spatial transcriptomics. It was the first time we were conducting this kind of omics at single-nucleus and tissue levels, so we sought strong support to avoid any pitfalls, he elaborates.

Earlier, the department had discussed hiring a bioinformatician but ultimately decided against it. Commercial service providers had also come up in the discussions and, among them, Genevia Technologies. When the analysis of Dr. Feraille’s omics data became a priority, he reached out to Genevia to discuss the possibility of using their services. He became convinced of the team’s competence, and soon after the video call, a contract was signed.

Efficient Collaboration

The quality of the support the Feraille group received did not disappoint. The project finished slightly quicker than anticipated, and the results were intriguing.

– The outcome was positive: we got some interesting results that aligned perfectly with the lab results. Genevia’s bioinformatician was very qualified, and the interaction between him and our team was good. He understood our objectives and what we were looking for very well, even though he was not a specialist in kidney cell biology. Alone, we could not have achieved such great results, he says and continues:

– The communication was great and everything was very transparent: we had access to all of the data in the format we wanted. Overall, everything went smoothly, and the collaboration was fruitful.

Impressed by his experience with Genevia's service and the strong results he received, Dr. Feraille has already recommended the company to his colleagues interested in incorporating similar experiments. He sees many advantages in using an external service provider for bioinformatics and emphasizes the importance of good communication between the bioinformatician and the research group.

– Obviously, one person cannot work miracles if he's not a specialist in your research topic, so for optimal results, you have to understand that this kind of collaboration is interactive, and you have to provide some input. I also learned a lot in the process: as a matter of fact, I was very surprised by how robust the data and how powerful the analysis were, he reflects.

– In the end, we are not generating enough data that it would make sense to hire a bioinformatician. On the other hand, if we shared a bioinformatician between several groups, we would have to compete for their time. Also, if you hire a single person, they will have some specialization but be weaker in other areas: with a company like Genevia, there is a team with a range of different competencies, and you can trust that they are always up to date. Last but not least, outsourcing this kind of work is, in fact, much more cost-effective.

– My experience with Genevia was positive, and I am very happy with the service. All of our goals were achieved, and we obtained the information we were seeking. I don't regret investing in this and will not hesitate to do it again if the need arises, Dr. Feraille concludes.

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