Conversation with Emmanuel Farge: Mechanics of Reprogramming the Embryo

Emmanuel Farge

With the ramping up of investigations in various parts of the world into the mechanics of biology, I’ve decided to post my conversation with Institut Curie biophysicist Emmanuel Farge on the role of mechanics in reprogramming the embryo, relating to his work first published in the scientific literature in 2003, which was well received by the science establishment.  

“People were rather ready for this,” Farge told me at the time of our 2010 interview that follows.

His perspective is one of development as “co-evolution of form and genome.”

Emmanuel Farge currently leads a team of biomedical researchers at Institut Curie in Paris.  The Farge group studies the mechanics and genetics of embryonic and tumor development. 

Emmanuel Farge’s PhD is in biophysics from Institut de Biologie Physico-Chimique and his undergraduate degree in physics from Université Paris Diderot.

February 15, 2010

Suzan Mazur: In 2003, your article in Current Biology showed how morphogenetic movement affects developmental genes.  You did an experiment in which you flattened a three-hour-old fruit fly and noted that mechanical force was necessary for gene expression and cell division.  You said you can reprogram the embryo mechanically at the beginning of its life and that mechanical induction may be an ancient mechanism for inducing gut formation, which could have evolved from a primitive reflex response to mechanical deformations.

Would you say a bit more about the experiment?

Emmanuel Farge:  Between 2003 and today we have new data in that field, so I will also explain our progress.  This paper, in fact, was designed to check a simple idea. 

We’ve known for 20 to 25 years, thanks to the work of Eric Wieschaus at Princeton and Maria Leptin in Europe—these two groups mostly.  There are other groups, but these are the most important ones.  They demonstrated that morphogenetic movements are closely controlled by patterning gene expression.  It means that during embryogenesis you have two kinds—

Suzan Mazur:  Are you reversing what you said in 2003?

Emmanuel Farge: Absolutely not.  I’m establishing the background.  I’m just saying that before I made this work, this is what was known. 

So, during these 20 to 25 years these groups have demonstrated that patterning genes control morphogenetic movement. Embryogenesis combines these two kinds of morphogenetic processes.  The first one is biochemical patterning, so you have to define domains of expression of genes that will give the polarities of the embryo.

We know embryogenesis combines biochemical patterning with morphogenetic movements.  You have to give a biochemical shape to the embryo.  What’s up.  What’s down.  What’s dorsal.  What’s ventral.  And you also have to generate a morphology, which is complex, to change the geometrical shape of the embryo. 

So, the background is that since 20-25 years, some groups have already found that patterning genes control the change of geometrical shape of the embryo. 

My feeling and my ideas at that time were that it was difficult to imagine the genome could not be aware of the shape it is in charge to develop, the geometrical shape.    

Suzan Mazur:  How do you define what a gene is.

Emmanuel Farge:  Well, I don’t really have clear ideas on this debate.  In fact, what’s a gene?  To me a gene is just a coding region that produces protein.  I know there are a lot of debates around that.  To me the most important point is that the proteins are real. 

These proteins have functions.  I would call the gene the complete process that leads to the expression of a protein.

Suzan Mazur:  What is your thinking about the origin of the gene?

Emmanuel Farge: I am not competent to answer this question.  I take the existence of this process, the existence of the protein expressed as it is, and my work is then to couple mechanics to genetics.  I’m not a specialist in this question of the origin of the gene.  I’m more pragmatic in my approaches.

I’m talking about genes and mechanical strain associated with morphogenetic movements. A morphogenetic movement is just a change of shape of the embryo.

Suzan Mazur:  Picking up on where we left off earlier—you were describing what was already known in the field and then in 2003 you did this experiment. 

Emmanuel Farge:  The experiment was really done to test whether the genome could detect the elaboration of shape of the embryo.  It was a quality control idea at the beginning.  It was difficult to imagine that during all these days the embryo develops with the genome giving orders to the shape without being able to detect at certain stages the state of the elaboration of this shape. 

The idea was because the output here is a shape, it’s not biochemical in nature.  It’s just a physical property.  So, the idea was really if such a feedback exists, the simplest way would be through patterning genes that are mechano-sensitive. You could modulate the expression of patterning genes, so modulate the state of expression of the genome as a function, as a shape that develops.  That was really the basic idea.

Testing this involved a very simple approach.  Taking an embryo just before it initiates its natural morphogenetic movements, changes, and just before gastrulation.  Gastrulation is the first stage of morphogenetic movements during embryogenesis.  Then squeezing the embryo gently to globally change its shape, and observing if the patterning of the embryo changes.  We wanted to see if we could change the pattern of expression of patterning genes.

Suzan Mazur:  And you found that—

Emmanuel Farge:  And we found that effectively was the case.

Suzan Mazur:  What did the embryo do?

Emmanuel Farge:  It generated the expression of ventral genes on the dorsal part of the embryo and all around the embryo.  So this really means that you induced, you forced the lateral and dorsal cells to become ventral.  All the cells that were fated to become dorsal and lateral under stress became ventral. And then of course the ventral cells should have invaginated.  This didn’t happen because all the cells around the embryo were forced to express ventral genes.

The most important point is really that all the mesoderm genes, the genes that encode for the ventralization of the tissue were expressed everywhere.  You transformed an embryo into a ventral tissue everywhere.

Suzan Mazur: You say mechanical induction may be an ancient mechanism for inducing gut formation.

Emmanuel Farge:  Yes.

Suzan Mazur:  What would have been the source of this ancient mechanical stress?

Emmanuel Farge: Perhaps I have to describe experiments we did in between. The first question is, is this property used in natural embryogenesis? If you demonstrate that you can manipulate the expression of a gene like Twist to external mechanical strains, it doesn’t mean that internal strains develop by morphogenetic movements of the embryo itself. 

We published a more recent paper in the journal Developmental Cell where we discuss that at the anterior pole of the embryo, when you look at natural embryogenesis, you have cells that are fated to give the anterior gut of the embryo and these cells before beginning to form the tube of the gut are compressed by natural morphogenetic movement of gastrulation. 

So, in fact, you have movement into the tissue, that is called germ-band extension.  This movement, in fact, is the extension of the ventral part of the embryo.  And because you have the ventral part of the embryo that extends, the anterior pole itself is compressed by this extension.

There is a response internally in response to natural movement, natural morphogenetic movement at the anterior pole.  What we noticed was that during the compression of the anterior pole cells by the germ-band extension, which is completely natural, independent of my manipulation, what you see is another expression of Twist, very strong, which correlates with the compression of these cells by the natural morphogenetic movement.of germ-band extension.

To test that this expression was mechanically induced by the compression, we made a laser ablation of some part of the tissue to unlink, to uncouple the ventral part of the tissue that led to the force that compresses the anterior pole. If you make this ablation, you have no more link.  No more mechanical link between the anterior pole and the tissue that extends.  Then you block the expression of the anterior pole.  If you look at the result you see that you do not anymore have the expression of Twist.

Then what you do is that you want to test this to see if you can rescue the expression of Twist by compressing it again.

Suzan Mazur: You’re concluding from these two experiments that it’s a combination of mechanical induction and gene expression.

Emmanuel Farge:  Exactly.  Because you need the gene expression to have the germ-band extension.  Then after you need the germ-band extension to have the expression of Twist at the anterior pole, which is mechanically induced. What I’m saying is that you always are in a situation where you cannot say that mechanics is more important than genetics and the reverse is true also.  You have a strong coupling between the two. 

Mechanics alone and physics alone is not enough.  Genetics alone is not enough.  Coupling both through mechanical induction allows us to understand this expression of Twist at the anterior pole of the embryo. 

What we found in 2008, in fact, is that this mechanical induction of Twist in stomodeum is necessary for the correct tissue organization and formation of the anterior gut.  If you don’t have this mechanical induction of Twist in the anterior pole cells, then the larva develops a gut but it does not express the good genes to make cells in order to digest.  It’s not functional.

Suzan Mazur: When your results were published in 2003, how was your work received by the science establishment?

Emmanuel Farge:  Quite well by a large majority of people, in the genetic field also. It was reviewed favorably in Nature.  It’s been reviewed a few times since 2003 in Science and in Nature.

In 2003, I was just saying that mechanical induction exists, that we have to add this property to the other known properties of development to better understand development.  I don’t have an approach that this is a major process, it was only additive.

People, in general, were quite open to the idea.  And geneticists thought it was time to see the mechanical approach, to try new things. 

I never saw anything but positive reviews in the major journals. The written feedback was always positive. For someone coming from biophysics and physics, it was a good sign from geneticists to have this feedback.  People were rather ready for this.  Of course, you cannot convince 100% of people.

Suzan Mazur:  You were the first to make this experiment?

Emmanuel Farge: In embryology, yes, I was. 

Suzan Mazur:  How do you view the debunking of Darwinian natural selection? That natural selection means there is a selector.

Emmanuel Farge:  In France in these last 10 years we’ve had a lot of research between physics and biology, but much more between physics and cell biology.  In terms of evolution, to my knowledge I don’t know a lot of people in Europe thinking about the involvement of physics in evolution.

Suzan Mazur:  Is that right?  There’s the Altenberg group at Konrad Lorentz Institute, who I’ve written about.  They view the gene as non-central.

Emmanuel Farge:  The gene being non-central is not the same.

Suzan Mazur:  They’re also taking a physical approach to biology.

Emmaneul Farge:  Okay.  It’s true from what we’ve found experimentally that a gene is not central.  But it does not mean that the gene is not important.  I try to not be theoretical in these approaches.  I try to have a pragmatic approach from the data I have because you can say and imagine many things and that’s very interesting, but the point is that in our lab we try to make experiments first and then see what we can say about them. 

We have two simple experiments.  The first one is the Twist mechano-sensitivity, which we discussed. And the second one, much more recent, that was published in Science in April 2009, we succeeded in triggering invagination of tissues just by poking tissues.  So we were really generating the phenotype of phagocyte in response to touch.  From this we have an experiment and we say okay we have an embryo which is very early so it could be equivalent to an ancient embryo and when we touch it gently, it tries to eat what it touches.   So that’s really in line with what I proposed in 2003.  It works a little bit differently than I thought at the beginning but still the phenotype is there.

What does that mean in terms of evolution? It means that maybe in ancient times there existed ancient embryos composed of many cells but that were not yet organisms.  And maybe when those embryos touched the ground due to gravity, they were sensing mechanical strains and they trained themselves to eat, phagocyte, to invaginate sediments.  Then maybe the mechanical activation of invagination is indeed the first eating response to touch.   And we have reactivated it experimentally in the lab.

What does that mean in terms of evolution if we are right?  That the emergence of this property of mechano-sensitivity leads to invagination.  What does that mean?  It means that from an aggregation of cells that were initially inert, that were not organisms only an aggregation of cells, you generate something like the first organism.  Because an organism is a structure of tissues that generate an organ.  If you don’t have an organ, you don’t have an organism.

Suzan Mazur:  What kind of genes would this mass of cells have at that point?

Emmanuel Farge: At that point, we don’t know.  This is still a speculation.  But in fact, you need a gene called Fog.  This gene leads to the mechano-sensitive response of the tissue.  What’s interesting is that Fog is under the control of Twist, so there is a coupling.  So if you have Twist, you have Fog. 

From the data we can propose that one day this gene was expressed and then it made the tissue active, mechano-sensing. This means that you may not have waited for Twist mechano-sensitivity for this invagination to be efficient.  You may only have first the Fog expression.  This was published in Science in 2009.

To end this story, because we are talking about evolution, and this is probably the most relevant part of the story leading up to evolution—we propose that one day appeared the expression of this Fog protein that made the tissue mechano-sensitive and able to generate an invagination.  The appearance of this mechano-sensitive gene Fog could have triggered the transition, the emergence of the first organism. Because you generate the first mouth.  The first gut.  Primitive, but the very first time cells behave collectively to generate an organ rather than simply being an inert collection of cells.

The second part, just to end the thoughts in terms of evolution—we imagine that one day the embryo did not wait for external mechanical strain to generate this primitive gut, primitive mouth and then it developed from the inside of its tissues its own morphogenetic movements.  So somehow genes were expressed.  And by pulling its own strength from the inside it triggered by itself the response of the tissue.  And then it generated by itself, its mouth. 

This is part of Lamarckism, in fact.

There is no inner region of anything but there is the trigger from the environment of the response that leads to the generation of an organ.  Then after evolution the embryo itself triggers this, replacing the external signal by an internal signal. It’s the beginning of embryogenesis.

Suzan Mazur:  Do you find resistance to the concept of evolution in France?

Emmanuel Farge:  No.  People in France don’t want to mix religion with science and politics.  It’s strongly separated.  We’ve had the religion wars in France.  When the religion wars stopped, we decided we should separate politics, science, and religion.

Suzan Mazur: But you don’t see a more physical approach to biology happening there in France and in Europe?

Emmanuel Farge: We do see it in cell biology since 10 years now as I mentioned earlier.  But in developmental biology, in France I don’t really see much of it.  Saying the gene is no more central is really what we have to do, but trying to minimize the importance of the genome, in my opinion, would be risky. 

We really have to take an approach that symmetrically studies the coupling of the genome properties and the physical properties.  What are the emergent properties, emergent physical processes from this coupling rather than trying to find that physics is more important or less important than the genome. 

It’s a question of—  Living matter has a genome, so it matters.  Living matter is composed of soft matter physical structures so this matters too.  Both appear to be very important and intricately coupled.  So I think that the sea change today is that effectively we have many more people reintroducing physics to the problem but often it seems to be a kind of reflex to say that physics is more important than the genome.  I’m not sure it’s a good approach. I prefer to think in terms of coupling rather than control of one over the other one.  To me, it’s a co-evolution of form and genome. 





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