Andres, can you introduce yourself and tell us how you arrived at the iBV?
I come from Colombia where I did an undergrad and a master in biomedical engineering. I learned mathematics, programming, medical image processing and statistics; but at the end of my undergrad I ended up developing algorithms to quantify wound healing images of cancer cells and doing molecular biology. I guess it happened this way because I became interested in the more biological part of my degree since the first semesters. At this point, I was very interested in using biophysics and mathematics to study cell biology and basic fundamental research, so I decided to look for a PhD position. During a short internship in Lyon, I met Szilvia Ecsedi who was a postdoc in Arnaud Hubstenberger’s lab. She drew my attention to a position opening in the lab, I contacted Arnaud and then we applied to a call from UniCA named “doctoral program of excellence”. I was selected and I could join Arnaud Hubstenberger’s team (created at the end of 2017) as his 1st PhD student in October 2018. The research project aimed to develop highly sensitive and quantitative imaging techniques to understand how mRNAs are coordinated to development. After 3 years, I could extend my thesis for another year thanks to a 4th year-fellowship from FRM.
Can you explain to us what is the scientific question you are interested in?
The big question we asked ourselves was “How millions of mRNAs are coordinated to cellular activity?”. In our case, we focused on the oocyte that can either be active (high activity) or quiescent (low activity) during its life. We were interested in: (1) which mRNAs are translated or repressed and what is their localization within the cell, (2) is the concentration of repressed mRNAs controlled, and (3) could this help the cell to maintain the homeostasis of mechanisms that control translation.
We determined that mRNAs, whose translation is repressed, can sense their own concentration: if they exceed a limit, the excess of mRNA copies self-assemble into “homotypic nanoclusters”. This compaction of repressed messenger copies of the same sequence identity allows the concentration of soluble copies to be robustly fixed. This is important because these soluble copies diffuse the information through the cell and they need to be easily controlled.
In oocytes with reduced activity, there is a second scale of regulation: different nanoclusters can co-assemble and form larger macro-condensates, building a huge, selective and dynamic storage in the cell. We think this happens because when cellular activity decreases, a large amount of mRNAs become repressed and they need to be co-coordinated. Macro-condensates provide a good center for this co-regulation and storage. There is a plus: stored mRNAs could be used later, for example, when the oocytes are being prepared for fertilization or in the embryo. We actually showed that individual mRNAs can be released from condensates when their translation is activated. In summary, assembly and release of mRNAs depend on translation activity and sequence identity.
Another important discovery from our work was that the buffering of repressed mRNAs into homotypic nanoclusters within macro-condensates enables a robust ratio between messengers RNAs and regulators in the cytoplasm, which can be important to maintain translation regulation across cellular activities, and even support quiescent oogenesis.
Why is that important?
We showed that condensates can protect against increased mRNA levels in a physiological context. A hallmark of many diseases is the deregulation of mRNA levels and especially those that shouldn’t be translated. Our findings could be very important in understanding additional ways in which such deregulations escape physiological control mechanisms.
For example, these dynamic condensates can transition to pathological aggregates which do not longer behave as protective mechanisms but instead they appear in human neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease. The clustering of mRNAs during viral infection or in cancerous tumors, is also probably a way to hijack the normal flux of mRNA information and transform the cell.
What could be the impact of your work for health?
We always hope that our work will be translated into something that could be beneficial for people’s health. There are a lot of efforts in targeting these pathological aggregates in neurodegenerative diseases. Our paper also expands a condensate purification technique developed by Arnaud for cells to C. elegans. We could imagine new ways of applying this purification technique to patients and find biomarkers and even therapeutic targets in cancer for example. Researchers are currently trying to use condensates and other types of phase transitions for drug discovery and delivery. In the US, biotech companies have recently raised millions of dollars to target RNA condensates in diseases. In general, phase transitions in biology is a young field but it has a lot of promising developments.
What are the remaining questions?
First, there are some technological challenges that need to be solved: tracking and measuring physical properties in vivo when you have a huge condensate is relatively simple, but measuring nanoclusters dynamics is more complex and has been so far limited even using the most advanced super-resolution microscopes.
Second, we need to understand what is the molecular grammar that guides mRNAs self-assembly: What are the sequence motifs bringing specificity? What prevents non-specific promiscuous aggregation between RNAs? Is self-assembly based on base-pairing?
Another idea is understanding how condensates can provide new solvent environments where the biochemistry can be different to what we are used to. What are the consequences on RNA behavior and reaction dynamics involving RNAs are still open questions.
What did you learn from your PhD?
I have learned the importance of thinking about the « big picture » and not to focus on partial things. I also enjoyed and learned a lot how to make good figures and present results in a way that people will understand easily, which was not so straightforward for me because I like mathematical representations and plots that are not necessarily the best way to go. Our team really cares about learning how to communicate results in a clear way, both oral and written, we all train a lot in these areas in a collaborative way.
What are your plans for the future?
I will leave the lab next year to do a post doc in a biophysics or super-resolution microscopy lab to understand more about the principles of phase transitions on single-molecule biology. I’m thinking about Germany but I do not know yet. It will probably be in Europe. I would like to be a researcher and have my own group if I find my niche in academic research.
Did you also enjoy other activities at the iBV or at the “Ecole Doctorale”?
Yes! I have met many friends, I have always felt very welcome and have enjoyed my stay, it was a good social experience!
What do you do for fun, out of the lab?
I like cycling, hiking, and running in the morning on the Prom. A few months ago, I went from Nice to Milan by bicycle, it took me one week!
Andres’s price will be awarded on December 8 during the Ecole Doctorale meeting.
To read more:
Andres and Arnaud’s article published in Cell:
Cardona, AH, Ecsedi, S, Khier, M, Yi, Z, Bahri, A, Ouertani, A et al. Self-demixing of mRNA copies buffers mRNA:mRNA and mRNA:regulator stoichiometries. Cell. 2023; doi: 10.1016/j.cell.2023.08.018. PubMed PMID:37703874 .
CNRS national communication: