10-30-18

The ‘Toulouse Cancer Santé’ Foundation, Inserm and the Pierre Fabre Research Institute launch the first Chair of bio-informatics in oncology for research into immuno-oncology at the Toulouse Oncopole

The ‘Toulouse Cancer Santé’ Foundation is dedicated to medical research on cancer and has been recognized as a public-interest foundation by the French State since May 5, 2006.

The Cancer Research Center of Toulouse (CRCT) is a joint research unit bringing together Inserm and University of Toulouse III-Paul Sabatier, comprising 20 teams, 4 of which are also accredited by the CNRS (French national center for scientific research).

The Cancer University Institute of Toulouse-Oncopole (IUCT-Oncopole) is a hospital with over 300 beds, exclusively dedicated to oncology patients, bringing together Toulouse University Hospital and Institut Claudius Regaud (cancer center).

As a longstanding partner of the Oncopole in Toulouse, Pierre Fabre Laboratories has made oncology its main focus of research and development in the pharmaceutical field.

 

The ‘Toulouse Cancer Santé’ Foundation, Inserm and the Pierre Fabre Research Institute, all three major players at the Toulouse Oncopole campus, have created the first Chair of Bio-informatics in Oncology for research into immuno-oncology. To head it, they appointed Vera Pancaldi, a physicist and systems biology expert, who took up the post at Inserm on September 3, 2018 at the Cancer Research Center of Toulouse (CRCT). Above and beyond the initiative launched today, the overall strategy of Inserm at the CRCT, the Cancer University Institute of Toulouse-Oncopole (IUCT-Oncopole) and Pierre Fabre is to strengthen public-private partnerships in oncology.

Co-construction by academics and industry

The creation of the Chair of Bio-informatics in Oncology will bring together the ‘Toulouse Cancer Santé’ Foundation, Inserm and the Pierre Fabre Research Institute (PFRI) for five years in a process of academic and industrial co-construction in research into immuno-oncology and translational medicine at the Toulouse Oncopole.

According to the Memorandum of Understanding and the Chair Agreement, the Pierre Fabre Research Institute and the ‘Toulouse Cancer Santé’ Foundation will each invest 1 million euros over five years (€200 000 per year). The Chair will be integrated with CRCT teams in the Inserm building at the Oncopole, which will provide the technical platforms and also contribute €335 000 to the project.

The Chair will be governed by a tripartite scientific committee, meeting up at least once yearly. It will comprise two members from PFRI, two members representing Inserm and two members appointed by the ‘Toulouse Cancer Santé’ Foundation.

Bio-informatics expertise at the core of the collaboration

The Chair will be occupied by Vera Pancaldi, an internationally-recognized researcher with a novel profile specialized in bio-informatics and system biology. Her current research is on cellular heterogeneity and 3D genome architecture at the Life Sciences department of the Computational Biology Group at the Barcelona Supercomputing Center (BSC).

With the Chair, the desire is to have a representative who is a leader in bio-informatics, for the CRCT to fulfill its aim of becoming an expert center in oncology data management. Vera Pancaldi's first task, therefore, will be to set up a team of five bio-informatics specialists (Masters and PhD level) to create a talent pool in this rapidly growing discipline.

Another positive is that she will occupy a pivotal position in the partnership dynamic, at the center of interaction between the CRCT, IUCT-Oncopole and PFRI. Vera Pancaldi will also have access to technical platforms at CRCT, particularly the bio-informatics facilities necessary for her research, as well as patient data collected by the hospital's doctors. She will also work directly with bio-informatics specialists from Pierre Fabre.

With the very concrete approach of this Chair, the aim is to accelerate the pace of development of new drugs going in the direction of personalized medicine. The CRCT and IUCT-Oncopole are thus prioritizing two areas of cooperation: data collection and analysis to facilitate choice of therapy and constitute data strings for internal projects, and identification of new genes that will be future biomarkers or therapeutic targets.

A plus for the partnership dynamic

In addition, the Chair will actively participate in scientific initiatives, publications and promotion of the CRCT and contribute to raising the Toulouse campus to a level of world-class excellence to attract talent from all over the world.

In her position as Chairholder, Vera Pancaldi's contribution will be twofold.

Firstly, she will continue to work with the Life Sciences department at the Barcelona Supercomputing Center (BSC), which was built around “Mare Nostrum”, one of the most powerful supercomputers in Europe. The Big Data approach is one of the BSC's main areas of expertise. The challenge of the future will be to exploit new Deep Learning and Artificial Intelligence (AI) approaches with the computer scientists and mathematicians at the Toulouse site.

Secondly, she will give fresh momentum to the networking dynamic at the Toulouse site. Because from now on, it is from Toulouse that Vera Pancaldi will drive the innovation dynamic of the Cambridge Networks Network, which she co-founded in September 2011, and which today brings together a community of 400 people interested in studying networks.

These strengths will help develop a whole ecosystem and a talent pool around the Chair at the Toulouse Oncopole campus. In this respect, the arrival of Vera Pancaldi is only a first step in the cooperation between Pierre Fabre and the Oncopole's academic and private structures, the future goal being to accelerate industrial partnerships in a spirit of open innovation.

“Big Data mining in a public-private partnership”

Alexandre Passioukov, Director of Translational Medicine, Pierre Fabre R&D

“Big Data mining has become a key source of innovation for the biomedical sector. This is true for both the academic world and the pharmaceutical industry. The ambitious project put forward by Vera Pancaldi, who is a bio-informatics expert, has clear synergies with our research and development work in oncology. Indeed, identifying response markers and discovering new therapeutic targets invariably involves analyzing huge quantities of “omics” data in relation to resistance to existing therapies. We are therefore delighted with the launch of this 5-year project with the CRCT and the ‘Toulouse Cancer Santé’ Foundation, a project that will be followed up by other collaborative initiatives in the context of Pierre Fabre's strategic alliances at the Toulouse Oncopole.”

“Bringing technical expertise to Big Data mining”

Gilles Favre, Scientific Director and Director of the Oncology Medical Biology Laboratory at the Cancer University Institute of Toulouse Oncopole (IUCT-Oncopole), Director of the Cancéropôle Grand Sud-Ouest (cancer research cluster in south west France), Director of the Cancer Research Center of Toulouse (CRCT) (Inserm/University of Toulouse III Paul Sabatier joint research unit and the CNRS-affiliated research team).

 

With the boom in the use of genomics big data in oncology, Vera Pancaldi is bringing new techniques for big data analysis to the CRCT. We have 22 000 genes and we are capable of sequencing them in full. We are also capable of knowing their expression. This amounts to several tens of thousands of messages transmitted by our platforms generating enormous quantities of data. In her research, Vera Pancaldi will be able to benefit from the CRCT's analyses of the single cell genome and single cell transcriptomics. We will be making our Wet Lab available to her for collecting and analyzing cells and molecular biology, as well as our Dry Lab for storing and managing data on computers. In the course of her research, she will work with computer scientists and mathematicians at the Toulouse site to go further in the construction of learning algorithms (deep learning, AI).”

“Enhance visibility and openness to the business world”

François Amalric, Managing Director of the ‘Toulouse Cancer Santé’ Foundation

 “For the ‘Toulouse Cancer Santé’ Foundation, the creation of this Chair is already a success with the arrival of an internationally-recognized data expert, who intends to transform this site into a center of excellence. The challenge is to develop expertise in bio-informatics with a view to forging new partnerships with industry players. The Chair will result in enhanced visibility for our research projects and greater openness to the business world.” 

“My research focus will be on tumor heterogeneity”

Vera Pancaldi, Chairholder, Bio-informatics in Oncology

Apart from her leading expertise in bio-informatics, what was impressive about Vera Pancaldi was her very international profile and her adaptability to current challenges in immuno-oncology research. Following her PhD in Physics of complex systems, she began work on fission yeast functional genomics in Prof. Bähler's laboratory at the Wellcome Trust Sanger Institute, and subsequently at University College London in England. “For me, there was no system more complex than living organisms,” she said. She continued as a post-doctoral researcher in plant epigenetics with Prof. Baulcombe's team at the University of Cambridge. Six years ago, she decided to embark on a new adventure in cancer research to take up the challenge of personalized medicine. She obtained a FEBS grant to join the Structural Biology and Bio-computing Group at the CNIO (national cancer research center) in Madrid, Spain. “I carried out research on mathematical modeling of tumor growth based on molecular data, she said. “I also started to get involved in BLUEPRINT, the European epigenome research project aiming to characterize the epigenome of different blood cells in healthy subjects.” This experience led her, last year, to take up her current position of researcher with the Computational Biology Group in the Life Sciences department of the Barcelona Supercomputing Center (BSC), where she carries out research on cellular heterogeneity and 3D genome architecture. She will continue to collaborate with the BSC and will participate in the Bioinfo4Women program. Her previous research on complex systems and epigenetics has been recognized and praised by her peers time and again.

On September 3, 2018, Vera Pancaldi took up the prestigious Chair of Bio-informatics in Oncology created by the ‘Toulouse Cancer Santé’ Foundation, Inserm and PFRI. “I am going to focus on researching tumor heterogeneity by simulating tumor evolution in its micro-environment,” she said. “The challenge also is to understand how the immune system interacts with the tumor.” In this area, Vera Pancaldi will work with Pierre Cordelier, Director of Research at Inserm and team leader at the CRCT, who is already working on pioneering research aiming to characterize pancreatic tumors at single cell level, particularly mobilization of an immune response to these tumors, which remain a serious public health problem due to their high resistance to current treatments. “The state-of-the-art technology at CRCT allows the various phenomena to be examined by studying the tumor at single cell level,” she continued.

This new position will also allow me to foster other collaborations with CRCT members, and also externally develop the center's public-private cooperation network in the targeted therapies field,” she concluded.