Temporal transcriptomics recording in single cells with FluidFM

Featured FluidFM user: Dr Orane Guillaume-Gentil
May 22, 2023 by
Temporal transcriptomics recording in single cells with FluidFM
Ilaria Di Meglio

Today, we introduce Orane Guillaume-Gentil, a long-standing user of the FluidFM® technology and pioneer of many FluidFM applications. Orane also developed the groundbreaking Live-Seq technique for temporal recording of transcriptomics in live single cells.

Orane Guillaume-Gentil, PhD. 
Deplancke Group, Laboratory of Systems Biology and Genetics.
EPFL. Lausanne, Switzerland

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Cytosurge: Hi Orane. Tell us a little about yourself; I’m curious to know about your background and what motivated you to pursue science?

OraneAs a child I loved all science – chemistry, biology, even archaeology – so I had a hard time selecting a subject to study at university. 

I chose pharmacy because it combines different sciences; you study how dysfunction can cause a disease and how you can devise effective treatments, how molecules interact and how you can deliver them to the right place with the right dose - with an attractive end-goal, curing diseases and helping patients. Then I had my first lab experience as an intern in molecular biology in the Zurich-PSC; it was a fantastic learning experience with a great supervisor, which initiated my motivation to pursue a career in research. Why? Because I understood that one part of research is driven by our curiosity, the other by the why and what it can bring to society. 

I went on to do a PhD in biomedical engineering with Janos Vörös, working on 3D tissues for regenerative medicine. Conducting research on such cutting-edge applications fascinated me, experiencing first-hand the incredible advances that can be achieved with new biotechnologies. However, the truth is also that it takes a lot of time and effort to fully develop a technology; you typically work for 3 to 5 years to reach a proof-of-principle stage, and share your research with fellow biomedical engineers, but beyond that, your research may never reach the people that stand to benefit from it. Not knowing if your work will be impactful can make research a little frustrating too. 

This was in great part what led me to start working with the FluidFM® technology - a unique opportunity to take the technology from its proof-of concept phase to a tool with real applications and impact in cell biology research.  

Cytosurge: And what motivated you to start working with FluidFM was the excitement at the prospect of developing a technology with true potential for biology?

OraneExactly. I joined the lab of Julia Vorholt as a postdoc in 2011, two years after the first FluidFM publication. At the time, the FluidFM showed immense potential for biological applications, but was still at the proof-of-concept stage. My aim was to further develop the technology, explore its potential use in biological research, and bring it to application stage, enabling its use in the biological community. After 10 years, I think we succeeded in developing a ground-breaking tool with a real potential to advance single-cell biology research.

Naturally, the path has not always been a smooth one. The first years involved a great deal of optimization, troubleshooting, probe design and engineering developments to make the technology functional. But once we managed to develop the first FluidFM applications – adhesion measurements, injection, and isolation of single cells [1-3] - we understood the huge potential of this technology. 

Another challenge along our journey was to convince the biology community of the potential of the FluidFM for life science research. We had a breakthrough when our publication in Cell on single-cell extraction [4] was released. This paper demonstrated the possibility of extracting picoliter volumes - the biopsy - from a single cell without affecting cell viability, paving the way towards live single-cell omics. Our work generated a great deal of interest, as it addressed a critical need in the field where cells are generally sacrificed during analysis. Indeed, the fact that we published this in a high-impact journal for biologists like Cell was an important validation from the biology community of the potential and impact that our approach could have in this field.

Cytosurge: Regarding this Cell publication and now that you have also published the Live-Seq story in Nature – both of which are extraordinary achievements – can you tell us about your experience in publishing in such high-impact journals? What are the costs and benefits?

OraneNow that both are done, I would say positive 😊 

As I mentioned before, the 2016 publication on single-cell extraction was really exciting. Not only is Cell a high-impact journal, it is also a journal with publications by and for biologists. For us this was an important validation of our work; and it showed that the FluidFM was no longer a specialized prototype instrument, but one with which you can really achieve and advance biology research. We captured the attention of biologists, and for me, this was the most gratifying. 

With the recent Nature paper, our Live-Seq story [5], the review process was particularly lengthy and challenging, as we had to convince reviewers of the reliability of our pioneering approach for single-cell transcriptomics. However, the overwhelmingly positive feedback we received from the community following the publication of our paper was extremely gratifying and further confirmed the large interest and demand for our approach.

I believe that the FluidFM is a remarkable technology for single-cell biology: it enables us to explore possibilities that could have only been imagined in science-fiction before, while meeting real needs in the field of biology, such as extracting picoliter-scale biopsies for transcriptome profiling all while keeping cells seemingly unperturbed.

Cytosurge: Can you tell us a little bit more about the Live-Seq technique and how this story came about?

OraneAfter our initial work on single-cell extraction with FluidFM, we knew that we could collect a single-cell biopsy while preserving the cell’s viability, and then transfer and process the biopsy to analyse the transcripts, proteins or metabolites. We realized that achieving single-cell molecular analysis without killing the cell could be ground-breaking, and focused on developing the approach for transcriptomics since the field was the most advanced in single-cell omics. However, since the biopsies are only a portion of entire cells, we needed a new protocol to analyse the minuscule amount of transcripts.

And, almost by chance, we got contacted by Bart Deplancke from EPFL, an expert in single-cell transcriptomics with a significant portion of his group’s research focused on stem cell biology. At the time, they wanted to understand why stem cells can take different fates, by recording their transcriptome before observing their fate. Yet all other single-cell transcriptomics techniques required cell lysis, making downstream observations of the cells impossible.  And this is how the collaboration that led to the development of Live-Seq began.

Cytosurge: What are your hopes with regards to live-seq advancing the field of transcriptomics? How does Live-Seq bring FluidFM forward and how does FluidFM advance your research and transcriptomics?

OraneNothing in biology happens in isolation - cells interact with each other and the surrounding environment in both space and in time - so there is a need for techniques that can measure spatially and temporally defined transcriptome profiles of single cells. 

Live-seq is complementary to existing single-cell RNA-seq technologies, unique in that it keeps cell alive and functional. It make it thus possible to capture the transcriptome of a cell prior to phenotyping or over the course of time. As such, it allows to address questions that no other scRNA-seq method can, such as how molecular and cellular heterogeneity is established, and what the actual (and not statistical) trajectory of cells is. Potential applications range widely, from studying disease progression to investigating the differential cellular responses to drugs, pathogens, or differentiation cues. In short, Live-seq provides a powerful tool with a wide range of research possibilities that are not accessible through other single-cell RNA-seq methods.

Regarding FluidFM, I believe that now is the perfect time for the technology to expand its reach and be utilized by researchers in a variety of biological fields, beyond biophysics. The technology offers a unique and powerful way to conduct single-cell research and help advance our understanding of biology.

Cytosurge:  FluidFM was invented 13 years ago and you have been part of the story since the early days (with 13 authored and co-authored publications on FluidFM!) so looking into the future: where do you see FluidFM 10 years from now?

OraneMy hope for the next ten years is that FluidFM is widely adopted by biologists as a powerful and versatile tool for manipulating and analysing single cells. Significant advances in the technology and its application have been made over the past decade, which I hope will trigger a large interest among biologists. In addition, the current development of the FluidFM OMNIUM system by Cytosurge, which makes the technology more user-friendly and with a greater degree of automation, is an exciting prospect that may aid in the diffusion of the technology within the biological community.

Find out more about Live-seq for transcriptomics recording of living single cells

Wanze Chen, Orane Guillaume-Gentil, Pernille Yde Rainer, Christoph G. Gäbelein, Wouter Saelens, Vincent Gardeux, Amanda Klaeger, Riccardo Dainese, Magda Zachara, Tomaso Zambelli, Julia A. Vorholt & Bart Deplancke. Live-seq enables temporal transcriptomic recording of single cells. (2022) Nature.

Illustration and representative images of the Live-seq sampling procedure using FluidFM (here, applied on brown preadipocyte IBA cells). The white arrows indicate the application of under- or overpressure. The black arrows indicate the amount of buffer and extract in the probe. Figure adapted from Chen et al. Nature 2022 (License: CC BY 4.0)


[1] E. Potthoff, O. Guillaume-Gentil, D. Ossola, J. Polesel-Maris, S. LeibundGut-Landmann, T. Zambelli & J.A. Vorholt. Rapid and Serial Quantification of Adhesion Forces of Yeast and Mammalian Cells. PLOS ONE, 7(12), e52712.

[2] O. Guillaume-Gentil, E. Potthoff, D. Ossola, P. Dörig, T. Zambelli & J.A. Vorholt. Force-controlled fluidic injection into single cell nuclei. Small, 9(11), 1904 — 1907.

[3] Guillaume-Gentil, O., Zambelli, T., & Vorholt, J. A. (2014). Isolation of single mammalian cells from adherent cultures by fluidic force microscopy. Lab on a Chip, 14(2), 402–414.

[4] Guillaume-Gentil, Orane, et al. "Tunable single-cell extraction for molecular analyses." Cell 166.2 (2016): 506-516.

[5] Chen, W., Guillaume-Gentil, O., Rainer, P.Y. et al. Live-seq enables temporal transcriptomic recording of single cells. Nature 608, 733–740 (2022). https://doi.org/10.1038/s41586-022-05046-9