CV Science

Emmanuel Farge Mechanical Induction of Developmental and Oncogenic Genes Expression

Course and current status

Trained as a physicist (U-Paris7 Magistère, 1984-89), switched to biophysics in the Physico-Chemistry Biology Institute Paris, in 1989 as a Ph.D. student with Philippe Devaux where he worked on the soft matter elastic response of biological membranes to biochemical active trans-membrane translocation of phospholipids ("flippase"), leading to endocytic-like vesiculation on liposome model systems (PhD, 1993). In 1994, he joined the Pasteur Institute in Paris (as assistant professor of U-Paris 7, 1993), where he showed with Alice Dautry-Varsat the motor role of the "flippase" in the endocytic vesiculation in living cells. He then moved on to head his own young investigator group at the Curie Institute in Paris in 1997 (Institut Universitaire de France, 99-04), modelling the mechanics of endocytosis in quantitative relation to living cells experiments, and demonstrating the mechanical induction of gene expression though the mechanical inhibition of morphogene endocytosis. In parallel, the Drosophila embryo was introduced to study the feedback role of the mechanical strains developed by gastrulation morphogenetic movements into the regulation of patterned gene expression, through the finding of the mechanical induction in Twist expression in the future anterior gut track cells, specifically strain compressed by the morphogenetic movement of convergent extension, and vital in functional anterior gut track development.

Currently, the Farge (Research Director Inserm, 2006) group combines the tools of genetics, experimental and in silico biomechanics to unravel the underlying mechanisms of biological molecular to mechanical multi-cellular phenotype interplay during embryonic morphogenesis and tumour development in vivo, involving mechanotransdcution driven cell collective effects, with evolutionary implications in the understanding of the evolutionary transition to endomesoderm (primitive gut) emergence in first metzoa. 

Health research implications consist in the finding of the reactivation of such ancestral embryonic mechanosensitive pathways in activating tumorigenic gene expression in the healthy tissues mechanically compressed by the growth pressure exerted by neighboring tumors in colorectal cancer, and searching for associated inhibitor treatments for innovative therapeutics. Such reactivation process was recently found to be an amplification by permanent tumor growth pressure of a process of mechanical stimulation of the physiological number of stem cells by physiological peristaltic like colonic myogenic mechanical pulsations, leading to a pathological increase in stem cells number with the production of cancer stem cells markers.

Scientific summary

The thematic of the Mechanics and Genetics of Embryonic and Tumour Development team focuses on the role of mechanical strain and deformation of macroscopic biological structures at the cell or multi-cellular level, into the regulation and the generation of active biochemical processes at the microscopic molecular cell level, including gene expression.

Endocytosis: vesicle budding driving force; mechanical modulation of endocytosis as a mechanotransduction process triggering transdifferentiation

Previously initiated on liposome mimetic systems (Farge and Devaux, Bioph J. 1992) and in cell culture (Farge, Bioph. J 1995; Farge et al, Am. J. Cell. Physiol., 1999), the first main thematic historically studied in the team was the motor role of biological membrane soft matter elasticity into the budding driving force of vesiculation initiating plasma membrane endocytosis (Rauch et al, Bioph. J, 2000).

Following, the role of mechanical inhibition of morphogenes endocytosis in the mechanical induction of transdifferentiation was found (Rauch et al, Am. J. Cell Phys, 2002). 

Developmental Biology: mechano-genetic/proteic reciprocal coupling activates gastrulation and regulates endoderm and mesoderm early differentiation of gastrulating embryos

Today, the team is investigating the role of mechanical strains and deformation associated to morphogenetic movements or tumour growth pressure on the surrounding healthy tissue, on the regulation of developmental genes expression movements during the early steps of embryonic development at gastrulation, and on the expression of oncogenes into the surrounding healthy tissue, respectively.

Specifically, embryonic development is a coordination of multi-cellular biochemical patterning and morphogenetic movements. Last decades revealed the close control of Myosin-II dependent biomechanical morphogenesis by patterning gene expression, with constant progress in the understanding of the underlying molecular mechanisms. We recently revealed reversed control of the Twist developmental gene expression and of Myosin-II patterning by the mechanical strains developed by morphogenetic movements at Drosophila gastrulation, through mechanotransduction processes involving the Armadillo/beta-catenin and the down-stream of Fog signalling pathways (due to mechanical inhibition of Fog endocytosis in this case), respectively. We used theoretical tools (simulations integrating the accumulated knowledge in the genetics of early embryonic development and morphogenesis), and  experimental tools (genetic and biophysical control of morphogenetic movements) to uncouple genetic inputs from mechanical inputs in the regulation of Twist meso-endoderm gene expression and Myosin-II patterning. Specifically, we set-up an innovative magnetic tweezers tool to measure and apply physiological strains and forces in vivo, allowing to mimic morphogenetic movements from the inside of the tissue in living embryos (Farge, Curr. Biol., 2003; Desprat et al, Dev Cell, 2008; Pouille et al Phys. Biol. 2008;  Ahmadi, Pouille et al, Science Signalling, 2009, Brunet, Bouclet et al, Nature Comm. 2013, Mitrossilis et al Nature Comm. 2017 Mechanotransductive cascade of Myo-II-dependent mesoderm and endoderm invaginations in embryo gastrulation).

Evo-Devo: a mechano-transductive origin of mesoderm emergence in the common ancestor of complex animals

More recently, we demonstrated the conservation of mechanical induction in mesoderm differentiation in both the zebrafish and Drosophila embryo, initiated by the mechanotransductive phosphorylation of the Y654 site of beta-catenin impairing its interaction with E-cadherins, leading to its release from the junctions to the cytoplasm and nuclei, and subsequently to the notail and twist earliest mesoderm target genes expression, respectively. The evolutionary origins of mesoderm emergence remains a major persisting opened question of Evo-Devo. Our results allowed to suggest mechanostransductive Y654 phosphorylation in response to first embryonic morphogenetic movements at the origin of mesoderm emergence in the 570 millions years ago common ancestor of bilaterians (Bouclet, Brunet et al, Nature Comm. 2013, http://www.nature.com/ncomms/2013/131127/ncomms3821/full/ncomms3821.html).

Evo-Devo: a more ancient mechanotransductive origin of endomesoderm specification and morphogenesis in first metazoan by environmental hydrodynamic marine mechanical strains

More recently, we found mechanotransductive induction of the endomesoderm gene fz10 expression via mechanical activation of Y654 phosphorylation by the morphogenetic movement of gastrulation in the cnidarian sea anemona Nematostella vectensis (N. vectensis), which common ancestor with the Bilateria dating back 600-700 million years. It is thought that endomesoderm patterning, ancestral to endoderm and mesoderm differentiation, probably specified the primitive gut tissues of first Metazoa over 700 million years ago.

We also found that mechanical stresses developed by marine hydrodynamic flow trigger gastrulation in early N.vectensis embryos in a Myo-II-dependent process, reminiscent of the mechanical stimulation of mesoderm invagination found in bilateria Drosophila embryos. In addition, we found Myo-II-dependent hydrodynamic stimulation of gastrulation-like inversion in Choanoeca flexa, a sister group to Metazoa whose common ancestor dates back more than 700 million years.

Our results thus suggest that the emergence of endomesoderm formation in early metazoans might have been stimulated in a mechanotransductive manner by environmental hydrodynamic marine mechanical constraints, leading to its Myo-II-dependent gastrulation, and to its subsequent gastrulation-induced Y654-bcat-dependent specification, in early metazoans (M.N. Nguyen, T. Merle et al., Front. Dev. Cell Biol. 2022).

Tumorigenesis: mechanical induction of tumourogenesis in healthy tissues, in response to the mechanical strains developped by tumourous growing tissues

We additionally found beta-catenin Y654 mechanical activation as leading to mechanical induction of oncogenes expression like Twist and Myc in colonic pre-tumourous  healthy tissues ex-vivo, in response to the tumour growth pressure of 1kPa (Whitehead et al, HFSPJ, 2008). 

We found beta-catenin Y654 mechanical activation as leading to  mechanical induction of oncogenes expression and tumour initiation in both pre-tumorous and wild type mice colon epithelia, in response to tumour growth pressure of 1kPa tumour growth pressure mimicked by both magnetic and genetic transgenic means in vivo  (M-E Fernandez-Sanchez, S. Barbier et al, Nature 2015 (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14329.html).

In this tumour setting, we found that the kinase that phosphorylates Y654-betacat is Ret. We found that Ret is furthermore itself mechanically activated (phosphorylated at its Y1032 site) (M-E Fernandez-Sanchez, S. Barbier et al, Nature 2015).

We additionally find that spontaneous myogenic pulses in the colon maintain physiological Stem cell levels via mechanical activation of the Ret/beta-cat pathway. And that this process is pathologically amplified by the added permanent pressure of hyperproliferation growth in the presence of tumours, leading to the doubling of Stem cells number mechanotranductively induced by Ret mechanical activation, and at the origin of mechanical induction of tumorigenesis (Nguyen Ho-Bouldoires, Sollier, Zamfirov et al Comm Biol. 2022 https://www.nature.com/articles/s42003-022-03079-4).

Molecular mechanotransductive activation of β-cat  in vivo

We found a key element of the mechanotranductive activation of the beta-catenin in vivo. In  Drosophila embryos, the mechanical constraints of gastrulation cause the opening of the major site Y654 of beta-catenin interaction with E-cadherin.

A 1nm streching between the alpha-helixes of beta-catenin and E-cadherin connected by Y654, under a force of 6pN applied to the complex, is predicted by molecular simulations to lead to the opening of the Y654 site in 15% of cases. Both the stetching and the opening are quantitatively observed expiermentally in FLIM and by anti-body accessibility increase to the Y654 site, in vivo. This initiates its phosphorylation by Src42A, then the activation of the downstream transduction pathway that leads to the expression of beta-catenin target genes like twist (J.C. Röper, D. Mitrossilis et al, e-LIFE, 2018).

For more details and for figures, see:

https://institut-curie.org/team/farge