Project stories: Interview with Antoine Khalil

Project stories: Interview with Antoine Khalil

In biomedical research, it is important to mimic the conditions that are found in our body. Traditionally, scientists have used 2D in vitro models where they grew cells on flat surfaces. However, as it can obviously be observed, the cells in our body are in three-dimension. So, wouldn’t it be amazing to create 3D models to study diseases, such as breast cancer?

Dr. Antoine Khalil and Mrs. Leonieke den Outer (master student) during confocal microscopy of cancer invasion in 3D matrices

Antoine Khalil is a senior Post-Doc at the UMC Utrecht in the Netherlands, in Johan de Rooij’s group. Their first and very important role at the Mechano·Control consortium was to establish the 3D in vitro models that recapitulate the characteristics of breast cancer in patients. They have used pieces of tumors (organoids) and grew them in 3D extracellular matrix (ECM). The ECM is a complex network of proteins that surround the cells in our body and provide important signals that control cell behavior. Antoine and his colleagues have characterized these cancer organoids and are trying to understand the nature of the extracellular matrix (ECM) that leads to cancer invasion and metastasis.

Working with organoids and 3D ECM makes in vitro studies more reliable, because they retain several aspects of tumor characteristics, and because most of the invasion that takes place in cancer patients, occurs in a 3D environment. The researchers can manipulate these organoids with the aim to stop the ability of cancer cells to become invasive and therefore, this will provide therapeutic opportunities to target the spread of the tumor cells throughout the body.  

“We use a new type of model system for our research that is called organoid culture. Organoids are made from biopsy materials that are isolated from breast tumors in human patients or mouse models. In this way, we can grow a piece of tumor in a controlled environment and study the effects of specific ECM conditions on the induction of tumor cell invasion”, explains Antoine.

Invasion and spread of breast cancer into the surrounding breast tissue often happen in groups of cells (collective invasion). The invasion of the cancer cell groups is driven and guided by few specialized cancer cells called the leader cells. Antoine and his colleagues have identified and fluorescently-tagged molecules that are exclusively expressed in those leader cells. They also found that several of these molecules are activated by changes in the ECM stiffness and tension. Thanks to that, several of these models and markers are being used by the other members and institutions of the Mechano·Control project.

Antoine and his colleagues aim to unravel the molecules that are most important in the transition to an invasive leader cell state and suggest methods to interfere with this process to prevent breast cancer invasion and metastasis.

The “life-time” of a tumor goes through different stages: In the first stage, the tumor grows in an uncontrolled fashion. In this stage the tumor is still confined and the cancer cells remain at their site of origin. At a later stage, some cancer cells within the tumor undergo a transformation that makes them motile and invasive. When this happens, tumor cells can spread to different regions in the body (including lungs, liver and brain) to form secondary tumors (metastases). That is why understanding how invasion is regulated will allow blocking it and this is very important to prevent and reduce metastasis.

It is now very well known that stiffer extracellular matrices surrounding breast tumors strongly associates with breast cancer invasion. “Our major task in the Mechano·control project is to unravel the molecular machinery in breast cancer cells that is essential for ECM sensing and the acquisition of invasive behavior”.

Figure 1. ECM-Dependent invasion of breast cancer organoids. Breast cancer organoids (MMTV-PYMT) embedded in 3D matrigel and collagen I. In both ECM conditions, the basal cells (yellow) are positioned at the tumor-ECM interface. Only in collagen I, the basal cells undergo a transition into protrusive leader cells and drive collective invasion (white arrowheads).

Until now, their data has established that only a pre-defined subset of breast tumor cells (the basal cells) (Figure 1, yellow) can become the leaders of invasion (Figure 1, white arrowheads). These leader cells drive the movement of groups of cancer cells. Antoine’s work shows that becoming a leader cell is triggered by changes in biochemical and mechanical properties of the ECM.

We found that dynamic bidirectional interactions take place between the leader cells and the ECM. Changes in ECM biomechanics induce protrusive behavior in cancer cells, which causes further changes in the ECM that becomes permissive for directional cancer cell movement. We have identified a set of genes whose expression is activated in response to increase in ECM stiffness; many of those genes regulate ECM remodeling and cellular invasive behavior.”

Antoine Khalil, UMCU

This work and much more is what Antoine and his colleagues in de Rooij’s team have achieved within the Mechano·Control project, and we know that there is more exciting and promising research to come until the project ends. For Antoine being a part of the Mechano·Control community was a great opportunity for his work because this project brings together various research fields at very different scales, “Throughout our meetings, conferences and communications we have established strong connections with the partners and learned so much from experts in the cell-ECM interaction field, at the computational, nanoscale and molecular and cellular levels” tells Antoine.

Project Stories: Interview with Samuel Pearson

Project Stories: Interview with Samuel Pearson

Samuel Pearson moved from Australia to Germany, where he works with research groups all over Europe with one common goal: to understand the factors influencing cancer progression. Samuel, Head of Applications in the “Dynamic Biomaterials” division of the Leibniz Institute for New Materials (INM), led by Prof. Aranzazu del Campo, is one of the Mechano·Control members. His work is focused on upscaling the production of polymer materials for 3D cell culture and bringing them towards commercialisation. Let’s take a closer look into his role within the consortium.

To understand how diseases like breast cancer develop, the response of breast cancer cells to different factors need to be studied one by one in isolation in 3D cultures. Samuel Pearson and his team produce synthetic hydrogels for 3D cell encapsulation with the possibility to adjust different parameters. These hydrogels mimic the properties of the natural breast cancer tissue in normal and disease conditions.

A particular interest of his group is the upscaling of the hydrogel precursors using affordable precursors and the design of stable, easy-to-handle compositions. This is the first step in technology transfer from the Mechano·Control project. With Mechano·Control partners, these materials are further developed into predictive breast cancer models.

Another crucial milestone for Samuel and his team is the processability of the hydrogels, which is related to the rate at which they are formed, i.e. the speed of the crosslinking reaction [1] during which cells are retained in a 3D matrix. The group has developed a patented crosslinking approach [2] based on thiol-methyl sulfone reactions which offer very convenient timescales for uniform encapsulation of cells. “In the future, we want to optimize our 3D cell encapsulation systems for automated high throughput methods that will enhance reproducibility and expand the applicability of our platform” explains Samuel. “The figure below shows how basal and luminal cells in breast cancer organoids organise in response to different adhesive ligands in the surrounding polymer network, which relies on consistent network properties” adds Samuel.


Figure 1: Invasive H7 breast cancer organoids were encapsulated in biofunctional hydrogels made from polymers developed at the Leibniz-INM. After 2 days of encapsulation, the effect of different bioactive ligands RGD and DGEA on polarization of the basal cells (stained with K14) and luminal cells (stained with K8) was explored. Scale bar = 50 um. Cell encapsulation and imaging were performed by Dr. Gulistan Kocer.

The materials developed by Samuel and his team play a crucial role in the Mechano·Control consortium. The high level of control and uniformity of the synthetic hydrogels allows to reduce the experimental variability in the biological studies, and this will help to uncover the individual factors that influence cancer progression. Moreover, this technology will not only be of great use for the consortium, but it also offers broad scientific and commercial potential for other 3D tissue culture models.

We are optimising polymer structure and crosslinking chemistry to make hydrogels with very reliable properties. The focus right now is upscaling to allow high throughput studies and moving towards commercialisation

Samuel Pearson

The Mechano·Control project brings together an interdisciplinary research community with the aim to understand and control how cells transmit and detect mechanical forces, from molecules to organs, and all the way up to the organism level. This requires developing and integrating disparate technologies, and each research group involved in the project is an expert in a very specific field and scale: “Each group has its own deep expertise, but because we are working towards a common goal everyone is really motivated to understand the contributions from the other partners, which deepens everyone’s knowledge and experience.”

Adrián de Miguel Jiménez synthesises polymer precursors used for 3D encapsulation of #tumour spheroids, based on the new methyl sulfone-based crosslinking chemistry developed at INM

[1] A crosslink is a bond that links one polymer chain to another, forming a network. Hydrogels are crosslinked networks of hydrophilic polymers that are swollen with water and widely used for 3D cell culture. The crosslink density is a key parameter that determines the mechanical properties of the hydrogel, which can in turn influence the behaviour of encapsulated cells. In the research described above, covalent crosslinks are formed using a patented thiol-methyl sulfone crosslinking reaction.


[2] del Campo, A.; Farrukh, A.; Paez, J. I. Novel Hydrogels. WO2021001203A1, 2021, Priority DE102019117997A 2019-07-03, Filed 2020-06-23, Published 2021-01-07.

Project Stories: Interview with Zanetta Kechagia

The Mechano·Control project aims to understand and control cellular mechanics from molecules to organs, and all the way up to the organism level. With this approach, its interdisciplinary research community will develop specific therapeutic approaches to tackle breast cancer. Zanetta Kechagia joined the Mechano·Control consortium from the first day that the project was launched. She is a postdoc in the team led by Pere Roca-Cusachs at IBEC, who is the principal investigator of the project.

Zanetta is focused on understanding the role of cell mechanics in the cellular and subcellular level. She is particularly interested on how extracellular matrix (ECM) composition and stiffness can jointly influence cell behaviour. “To achieve this, we are using a series of molecular and mechanical perturbations to unravel the role of specific cell-ECM interactions in shaping cellular mechanoresponses” explains Zanetta. 

Mammary gland epithelial cells. In cyan Intermediate filaments and red integrin β4. Scale bar: 20um (Picture by: Zanetta Kechagia)

Currently, she and other researchers at Roca-Cusachs’ lab are trying to identify which cell-ECM interactions can alter the mechanical properties of the cell cytoskeleton. To do so, she uses optical tweezers to perform oscillatory rheological studies, probing cytoskeletal mechanoresponses that are specific for different extracellular molecular components.

“We have found that cells respond to stiffness differently on different ECM substrates and that integrin molecules are key mediators of such responses. By using different ECM coatings, we can probe specific integrin interactions and record changes in the viscoelastic properties of the cytoskeleton over time.” – Zanetta Kechagia, PostDoc at IBEC

Mechanical forces greatly influence cell behaviour, for example in determining whether they differentiate, proliferate, or adopt a malignant phenotype. Understanding how molecular interactions can lead to changes in cell mechanical properties is a fundamental step in order to understand how mechanics control cellular behaviour and eventually tissue responses and cancer progression.

To meet this end, Zanetta is performing these experiments using breast epithelial cell lines with the aim to validate them at the organoid and tissue level, with the help of the other consortium partners. The Mechano·control project covers all scales, starting from single molecule nanotechnology at the smallest scale, to organoids and animal models at the organism scale to uncover cell responses to force at every scale.

Mechano·Control brings together very distinct but complementary research fields and scientists of the highest calibre in their respective fields. For Zanetta, joining the Mechano·Control project has been a great experience so far. “I had the chance to participate in several meetings, visit the partner institutions and discuss my work with our colleagues.  This helped me to acquire new knowledge and new research ideas to rise. One such exceptional experience was the summer school organised by Mechano·Control in 2019, where all the partners had the chance to exchange research ideas and present their work to an international audience.”

Mechano·Control featured at the Winter Issue of the EU Research Magazine

Mechano·Control featured at the Winter Issue of the EU Research Magazine

How do forces affect cell behavior? The Mechano·Control project is featured with a one page article in the EU Research Magazine in the “Winter’s Issue: Cellular and Molecular Biology research“.

Pere Roca-Cusachs, PI of the project, explains in this article the aim of the Mechano·Control project which is understanding the mechanical control of the biological function in order to abrogate breast tumour progression.

The consortium addresses this challenge thanks to an interdisciplinary research community with the aim of understanding cancer biomechanics from the single molecule to the whole organ scale. Ultimately, it’s hoped that the project will lead to the development of breast cancer treatments based on the new discoveries.

“Cells change their behaviour when they are in a stiff place; they further stiffen the tissue by secreting more matrix. If you convince the cells that they’re not in a stiff place, then they will stop secreting this, and this may help restore the normal stiffness of the tissue”

Pere Roca-Cusachs

“What happens if we change the composition of the extra-cellular matrix to look more like cancer? What changes?” asks Roca-Cusachs. “We are developing mimics of this matrix, where we can dynamically change their properties. We can make the matrix get stiffer or softer by applying different kinds of light.”

Pere Roca-Cusachs

You can read the article here:

We want to thank the EU Research Magazine for the article (EU Research WIN20/P17.)

Great success of the 2019 Mechano·Control outreach activities

This past 2019 has been a great success concerning the outreach activities carried out within the Mechano·Control project. More than 320 people attended talks, workshops, discussions… related to mechanobiology.

Each year IBEC organises several workshops on mechanobiology where students explore how cells exert forces and they measure them and also create a cell membrane model. This year three schools with 25 students each have participated in this programme. Also, once a year 24 students that participate in a larger programme called “Crazy about bioengineering” come to Pere Roca-Cusachs and Trepat’s lab to do hands-on sessions on how cells perceive the surrounding environment, mechanobiology and biochemical responses.

King’s College London participated at the 2019 Pint of Science with a talk on how forces are key to unveiling how life functions with an audience of more than 50 people from different ages and backgrounds.

UMCU organised three presentations throughout the year addressed to patients and general public about their research line on breast cancer, where more than 130 attended the meetings.

Last but not least, INM also organised two experimental activities at their laboratories reaching 40 students and also mentoring lab practice to 5 secondary school students.

PROJECTS STORY: The study of mechanical forces opens a promising front in the fight against cancer

Pere Roca-Cusachs, coordinator of the Mechano·Control project and PI at the Institute for Bioengineering of Catalonia has been interviewed for the European Comission Digital Single Market news section.

Through the interview by Giordano Zambelli, Pere unfolds the aim of the project and it’s impact to society and also explains his experience working with FET.

Finding effective solutions to fight cancer is undoubtedly one of the main scientific challenges worldwide, whose success needs necessarily to build on innovative pathways of research. Mechano-Control aims to understand the physical forces that determine the spread of a wide range of diseases, with potentially vast impact on the development of new therapies.

Read the full interview here: The study of mechanical forces opens a promising front in the fight against cancer

Mechanobiology of Cancer Summer School 2019

The MECHANO·CONTROL consortium, led by several research institutions across Europe, is launching a Summer School that will be taking place between 17-20 of September 2019 at the Eco Resort in La Cerdanya. The aim of the summer school is to provide training on mechanobiology, and specifically its application to breast cancer. This school will include lectures as well as practical workshops in different techniques and disciplines, ranging from modelling to biomechanics to cancer biology.

There will be scientific sessions in the morning, mixing 6 keynote speakers with 18 short talks selected from abstract submissions by junior scientists attending the school. In the afternoon, there will be 2-3-hour practical workshops, given by scientists from the MECHANO·CONTROL consortium. The course will also include leisure activities.

The 6 confirmed speakers who will attend the summer school are:

Marija Plodinec (University Hospital Basel)
Andrew Ewald (Johns Hopkins University School of Medicine)
Peter Friedl (Radboud University Nijmegen)
Guillaume Salbreux (Francis Crick Institute)
Christina Scheel (Institute of Stem Cell Research, Helmholtz Center Munich)
Buzz Baum (Medical Research Council Laboratory for Molecular Cell Biology at UCL)

ORGANIZING COMMITTEE:
Pere Roca Cusachs, Institute for Bioengineering of Catalonia (chair)
Xavier Trepat, Institute for Bioengineering of Catalonia (co-chair)
Marino Arroyo, Technical University of Catalonia-BarcelonaTech and Institute for Bioengineering of Catalonia (co-chair)

Binucleated cells could be the key in heart regeneration

A research team led by the IBEC, in collaboration with the CMR [B], discovers a mechanism that generates binucleated cells.This mechanism has been identified during the regeneration of the heart of the zebrafish, and could be associated with the extraordinary regenerative power of this animal.

Cells of the epicardium of the zebrafish with two nuclei (in blue)

After an acute heart lesion, such as a myocardial infarction, the human heart is unable to regenerate. The adult cardiac cells cannot grow and divide to replace the damaged ones, and the lesion becomes irreversible. But this does not happen in all animals. A freshwater fish native to Southeast Asia, known as a zebrafish, can completely regenerate its heart even after 20% ventricular amputation.

This extraordinary regenerative capacity has attracted the attention of researchers from all over the world, who see the range of possibilities that would be opened up if this mechanism of cell regeneration could be applied in human therapies.

In an article published today in the Nature Materials journal, a team of researchers from the Institute of Bioengineering of Catalonia (IBEC) led by Xavier Trepat, in collaboration with the Centre for Regenerative Medicine in Barcelona (CMR [B]), have discovered a surprising mechanism by which zebrafish heart cells move and divide during regeneration.

Researchers have focused on the epicardium, which is the layer of cells on the outer surface of the heart. Although the epicardium cells represent only a small fraction of the heart’s mass, they play a fundamental role in its regeneration. “The epicardium is the origin of several of the heart’s cell types, and secretes biochemical signals that tell the cells what they have to do at all times. It’s a kind of regeneration ‘hub’”, states Angel Raya, ICREA Researcher and director of CMRB.

After a heart lesion, the epicardium cells begin to divide and move en masse to cover the wound. Researchers have observed that, during this process, the cells become binucleated: they duplicate the genetic material and separate it into two nuclei, but they are not divided into two independent cells. “We were very surprised to discover cells that, instead of having one nucleus, as is the case in most tissues, they have two nuclei, and each of them contains a copy of the cell’s DNA” says Trepat, ICREA researcher at IBEC and associate professor of the University of Barcelona.

Researchers have discovered that the mechanism by which cells become binucleated has a biomechanical origin. Once DNA has already separated into two nuclei, most animal cells form a contractile ring at its centre. As it contracts, this ring divides the mother cell into two daughter cells. In the case of the heart cells of the zebrafish, the study shows that the ring adheres to the fibres of its environment so that it cannot tighten. The result is that the two daughter cells cannot separate despite having correctly duplicated their DNA.

“Multinucleation is a well-known phenomenon in cancer, because it is a cause of genetic instability. In other words, cancer cells lose control of the proteins they synthesise and behave pathologically. In the case of the heart of zebrafish, the multinucleation is physiological and does not seem to cause any problem”, states Marina Uroz, the article’s main author. The next step will be to study the role of multinucleated cells during the regeneration of the heart and other organs.

Dr. Trepat and Dr. Raya are part of CIBER-BBN (Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine)

Pere Roca-Cusachs and Antoine Khalil participate at the 2019 Gordon Research Conference

Pere Roca-Cusachs and Antoina Khalil in Lucca during the GRC

Last 5th-10th May was held the 2019 Gordon Research Conference on “Fibronectin, Integrins and Related Molecules” where Pere Roca-Cusachs from IBEC and Antoine Khalil from UMCU presented talks discussing Mechanocontrol results on how mechanical signals and the extracellular matrix regulate cell responses and tumour invasion. During the keynote session titled “Mechanisms and Mechanics of Integrin ECM Connections” Pere Roca-Cusachs gave a talk on “Exploring the Substrate Dependence of Integrin-Mediated Mechanotransduction”. Antoine gave an oral presentation where he described how cell-ECM adhesion regulates the positioning of basal cells and their specification into invasive leader cells during collective invasion of breast cancer organoids.

The Gordon Research Conference was held in Lucca, Italy and is the premier international conference for academic, government and industry scientists interested in understanding how integrins and the extracellular matrix regulate virtually every aspect of cell and tissue function. The program of the conference reflected the interdisciplinary nature of the integrin and extracellular matrix field, spanning different areas of biology from inflammation to mechanobiology, cell migration, stem cells, development, and cancer. During the meeting unpublished data was highlighted and stimulated active discussion among all participants.

Registration for Mechanobiology of Cancer Summer School 2019 is now opened

The MECHANO·CONTROL consortuium is launching the website for the “Mechanobiology of Cancer Summer School 2019” for the application process and registration.

The application period opens today until the 8th May 2019, where you can submint an abstract if you are interested in giving a short talk during the summer school.

The application does not guarantee acceptance to the Summer School due to the limited number of participants, an email with the resolution of the applicaton process will be sent on June 15th 2019.

The summer school will be held in La Cerdanya at the Eco-Resort located in Prullans in the Catalan Pyrenees.

The participation fee is 300€ (taxes not included) and includes accomodation in shared double room (from 17th-20th September 2019), full-board, workshops and conferences, leisure activities and shuttle bus from Barcelona to the venue.