ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Fabienne De Graeve is first author on ‘ An image-based RNAi screen identifies the EGFR signaling pathway as a regulator of Imp RNP granules’, published in JCS. Fabienne is an Assistant Professor in the lab of Florence Besse at Institut de Biologie Valrose, Nice, France, where she is interested in the molecular mechanisms regulating the spatial distribution of mRNAs.
Fabienne De Graeve
How would you explain the main findings of your paper in lay terms?
We are interested in cytoplasmic ribonucleoprotein (RNP) granules, which selectively and reversibly concentrate RNA molecules and regulatory proteins, contributing to the spatiotemporal regulation of the associated RNAs. Although the molecular and chemical bases of their formation are well understood, how their assembly and disassembly are regulated in a cellular context are still largely unknown. We addressed this question by searching for regulators of transport RNP granules characterized by the presence of the evolutionarily conserved fly RNA-binding protein (RBP) Imp (a homolog of mammalian IGF2BP). Combining an RNAi approach, which allowed us to suppress expression of many different genes individually, with an image-based high throughput screen in cultured fruit fly cells, we identified several dozens of genes that regulate the number of Imp+ RNP granules, including components of the MAPK signaling pathway. We have further shown that EGFR signaling favors Imp+ RNP granule disassembly through activation of the MAPK-ERK pathway and identified an important phosphosite on Imp.
Were there any specific challenges associated with this project? If so, how did you overcome them?
For this project, we had to extract information from hundreds of thousands of complex images. We overcame this challenge by collaborating with our colleagues in mathematics and computer science.
When doing the research, did you have a particular result or ‘eureka’ moment that has stuck with you?
In this project, conducting our screen quality control and developing the SPaDe algorithm, which detects small particles such as RNPs in images of cells, were great moments. These were carried out with the help of our colleagues in mathematics and computer science, Eric Debreuve, Xavier Descombes and two masters students, Djampa and Nicolas. Djampa's work enabled the visualization of cell survival rate in the 384-well plates used in the screen. Nicolas developed the SPaDe algorithm to detect the Imp+ RNP granules in the images from the screen. Both Djampa and Nicolas graduated successfully, and we were able to continue with our study. If I may say so, we were very happy to have had many students working with us on this project who are authors on this paper. Kavya and Paul are pursuing research in the academic field as a post-doc and PhD student, respectively, and Jeshlee, Djampa and Nicolas have joined private companies.
To identify genes that regulate the number of cytoplasmic GFP-Imp+ condensates, we combined an RNAi approach with an image-based high throughput screen in cultured Drosophila cells. We developed a pipeline to identify healthy cells on the basis of nuclei detection, followed by selection of cells with intermediate GFP–Imp expression levels and detection of GFP–Imp+ RNP granules to determine their number per cell and the GFP-Imp partitioning coefficient. In this image, masks of GFP–Imp+ cytoplasmic condensates were superimposed on the mask of their healthy parent cell.
To identify genes that regulate the number of cytoplasmic GFP-Imp+ condensates, we combined an RNAi approach with an image-based high throughput screen in cultured Drosophila cells. We developed a pipeline to identify healthy cells on the basis of nuclei detection, followed by selection of cells with intermediate GFP–Imp expression levels and detection of GFP–Imp+ RNP granules to determine their number per cell and the GFP-Imp partitioning coefficient. In this image, masks of GFP–Imp+ cytoplasmic condensates were superimposed on the mask of their healthy parent cell.
Why did you choose Journal of Cell Science for your paper?
We chose JCS because this journal covers many aspects of cell biology and is read by a large community of readers. The review process is fast. We are very happy that our study was accepted.
Have you had any significant mentors who have helped you beyond supervision in the lab? How was their guidance special?
Throughout my career, I’ve been lucky to meet many beautiful people. Here, I'll mention only two of them. The first is my thesis supervisor, Prof. C. Kédinger. In his laboratory, I learned scientific rigor. The second is Dr F. Besse. One of her strengths is to be always constructive.
What motivated you to pursue a career in science, and what have been the most interesting moments on the path that led you to where you are now?
Science is first and foremost a passion for me. It is nice to accomplish experiments to reveal the invisible and understand the hows and whys of biology. I also enjoy bringing together complementary talents or taking different approaches to address a question and realizing that they can converge towards a common result.
What's next for you?
Spatial transcriptomics, collaborations, and more challenges!
Fabienne De Graeve's contact details: Institut de Biologie Valrose, 28 avenue Valrose, 06108 Nice Cedex 2, France.
E-mail: [email protected]
