INTEGRATING MULTI-OMICS AND BIOLOGICAL KNOWLEDGE TO BRIDGE SIGNALLING AND METABOLISM

On Friday, March 22nd, Aurélien Dugourd from the Saez-Rogriguez lab, Heidelberg University will give a talk on how the integration of multi-omics and biological knowledge can bridge signalling and metabolism at 11am in Salle Cazaux, CRCT.

BIO: After he graduated from his Computational Biology master’s degree in 2015, Aurelien Dugourd joined Julio Saez-Rodriguez team as a PhD student. He worked on the development of hybrid mechanistic models, integrating gene regulation, signaling pathways and metabolomics data to explain disease phenotypes, help find new therapeutic targets and predict their potential effect based on a specific patient profile. This led to the development of the tools COSMOS and oCEan. This project was part of the collaborative SyMBioSys ITN project, financed by the European Marie Skłodowska-Curie actions, as well as the SMART-CARE consortium to apply mass-spectrometry-based systems medicine to cancer.
Today, he leads the development and application of methods to extract interpretable mechanistic insights from multi-omic datasets. He especially focuses on leveraging prior knowledge, in the context of signaling and metabolism of complex diseases, such as cancer and development of treatment resistance. He works in collaboration with pharmaceutical partners, notably Pfizer, to support the development of novel cancer treatments and better understand the development of resistances by bringing those methods closer to relevant industrial applications.

Follow the event online here.

Our 2024 call for PhD proposals is open

2024 Call for PhD proposals

 

The CARe Graduate School’s PhD program is devoted to the training of students in multidisciplinary research topics, from basic science to clinical or pharmacological applications, with a focus on cancer, ageing and/or rejuvenation. PhD research projects are directed by CARe-associated research teams from academic laboratories or partner companies. The EUR CARe PhD program selection will have two phases:

Phase 1: PhD pre-proposals will be submitted to Claire Mendoza (claire.mendoza-berrio@univ-tlse3.fr) and Clemence Grosnit (clemence.grosnit@univ-tlse3.fr) using this template, before evaluation and selection by the CARe Scientific Committee. Deadline for application is March 1st, 2024.

The applications must fall in the field of cancer, aging and/or rejuvenation. In addition, multidisciplinary is highly recommended and proposals must be at the interface of biology and mathematics, computer science, chemistry or physics. Examples are: mathematicians addressing complex biological questions by developing new molecules, tools, technologies or models, possibly doing some bench work, or biologists trained in mathematics, physics, computer sciences, advanced bioinformatics to develop new strategies that would be later questioned/validated in experimental biological settings…

Partnerships between teams from different doctoral schools, and/or foreign universities or industry are strongly encouraged (see scoring below). A short internship abroad (3 to 6-month) is mandatory, the nature of which should be briefly mentioned at this step. The travel and accommodation will be funded by the CARe program.

The scoring system (out of 10) is the following: 

  • Scientific quality of the proposal (5 points)
  • Co-supervision & interdisciplinarity (options 1 to 3 are not cumulative)
    1. If the project involves co-supervision by two teams working on different themes, each affiliated to a distinct disciplinary doctoral school : 2 points (lowest score)
    2. Or if the project includes co-supervision with an industry partner or a foreign university : 3 points (middle score)
    3. Or if the project involves co-supervision with an industry partner or a foreign university, spanning two interdisciplinary fields : 5 points (highest score).

NB: the candidates should not be formally identified at this step.

Upon acceptance, the proposers will be informed on March 11th, 2024, and the proposals will be posted online on CARe’s website and social networks.

Phase 2: PhD candidates for the pre-selected projects will submit the full proposal to Claire Mendoza (claire.mendoza-berrio@univ-tlse3.fr) and Clemence Grosnit (clemence.grosnit@univ-tlse3.fr) using the template that will be made available on CARe’s website.

At this step, PhD candidate must be identified and are asked to send a complete CV. In addition, it is mandatory to provide a full description of the 3-6 months internship, including a signed attestation from the hosting foreign university or from industry.

The files must be submitted as a single PDF before May 10th, 2024. Applicants will defend their proposal in early June 2024, in front of a jury representative of the CARe Graduate School, with delegates from Toulouse partner doctoral schools.

The audition will consist of 12 minutes of presentation and 15 minutes of questions. The presentation and the answers to questions have to be done in English.

The presentation must include, in this order, 1 title slide, 1 slide presenting the candidate, one slide presenting a previous research experience. The rest of the slides are dedicated to the presentation of the project (scientific justification of the research project, strategy, methodology, feasibility and risk management), including a description of the internship abroad or in industry. The following criteria will be evaluated by the jury: discussion of a previous research experience, quality of the oral presentation and of the response to questions.

SYMPOSIUM: Computational approaches for predictive immunotherapy

On Thursday December 21st, Dr Elana Fertig and Dr. Federica Eduati are giving a keynote lecture on Computational Sciences at IUCT-Amphitheater from 2pm to 4pm.

Dr Elana Fertig advances a new predictive medicine paradigm for oncology by converging systems biology with translational technology development. Her computational cancer biology research is inspired by her background as a NASA fellow in weather prediction. She aims to invent computational techniques that use multi-platform high-throughput precancer and tumor datasets to forecast the cellular and molecular pathways of future cancer progression and therapeutic resistance. An authority in computational oncology, Dr. Fertig has been a leader in establishing spatial multi-omics technologies, matrix factorization, and transfer learning as current mainstays in bioinformatics. Her combined expertise in computational oncology, chaos theory, nonlinear dynamics, and tumor immunotherapy ensure translational relevance and mechanistic validation of computational findings. Beyond algorithm development, Dr. Fertig’s transdisciplinary expertise enables her to lead large-scale, team-science projects adapting cutting-edge molecular profiling technologies to human clinical trials to uncover new therapeutic interception pathways. Her transdisciplinary research has made her a sought after mentor and recognized leader of new training paradigms that converge oncologists, pathologists, basic biologists, computational investigators, and engineers to advance the next generation of computationally-driven oncology care.

Dr. Fertig is a Professor of Oncology and Division and Associate Cancer Center Director in Quantitative Sciences, Co-Director of the Convergence Institute, and Co-Director of the Single-Cell Training and Analysis Center at Johns Hopkins University. She has secondary appointments in Biomedical Engineering and Applied Mathematics and Statistics, affiliations in the AI-X Foundry, Institute of Computational Medicine, Center for Computational Genomics, Machine Learning, Mathematical Institute for Data Science, and the Center for Computational Biology and is a Daniel Nathans Scientific Innovator and MD Cancer Moonshot Senior Scholar. Prior to entering the field of computational cancer biology, Dr Fertig was a NASA research fellow in numerical weather prediction.

Dr. Fertig’s research is featured in over numerous peer-reviewed publications, R/Bioconductor packages, and competitive funding portfolio as PI and co-I. Notably, she led the team that won the HPN-DREAM8 algorithm to predict phospho-proteomic trajectories from therapeutic response in cancer cells and was elected to the College of Fellows American Institute for Medical and Biomedical Engineering (AIMBE) in 2022. She serves on the editorial boards of PLoS Computational Biology, Cell Systems, ImmunoInformatics, and Cancer Research Communications.

Dr. Federica Eduati earned her PhD in Biomedical Engineering in 2013 working on different computational modeling approaches to gain new insights into biological systems. She then became a postdoc (EMBL EIPOD, co-funded Marie Curie fellowship) at the European Molecular Biology Laboratory (EMBL), shared between the Systems Biomedicine group of Julio Saez-Rodriguez at EMBL-EBI (Cambridge, UK) and the microfluidics group of Christoph Merten at EMBL-HD (Heidelberg, Germany). During her postdoc she led pioneering work on developing predictive personalized models of intracellular signaling pathways of cancer patients, combining mathematical modeling and microfluidics technology development. Since 2018 she leads the Systems Biolgy for Oncology group at Eindhoven University of Technology (TU/e, The Netherlands) as tenured Assistant Professor. The work of her group is focused on understanding drug response in the tumor microenvironment using holistic approaches to improve precision (immuno)oncology.

Tumors are dynamic ecosystems shaped by a multitude of interacting molecules and cells. The heterogeneity observed in patients’ tumor development and treatment responses can be attributed to diversity in the underlying regulatory networks. In this presentation, I will illustrate how mathematical models can provide a nuanced description and understanding of the intricate relationship between a tumor’s composition and its behavior. Using mathematical models, we integrate general prior knowledge on possible interactions and patient-specific data to gain a mechanistic understanding of resistance/response to treatment in individual patients. This approach holds the potential to improve the way we personalize treatment based on patient’s molecular characteristic.

Title of the conference: “Computational modelling of the tumor and its microenvironment for precision oncology”

Abstract: Tumors are dynamic ecosystems shaped by a multitude of interacting molecules and cells. The heterogeneity observed in patients’ tumor development and treatment responses can be attributed to diversity in the underlying regulatory networks. In this presentation, I will illustrate how mathematical models can provide a nuanced description and understanding of the intricate relationship between a tumor’s composition and its behavior. Using mathematical models, we integrate general prior knowledge on possible interactions and patient-specific data to gain a mechanistic understanding of resistance/response to treatment in individual patients. This approach holds the potential to improve the way we personalize treatment based on patient’s molecular characteristic.

Please join online here.

Research and Technology National Agency (ANRT) “Pour un plan national en faveur du doctorat” with CARe’s Director, Philippe Valet

The conference “Pour un plan national en faveur du doctorat” (For a national plan to promote doctorates) was held on Friday 17 November at CampusCyber – La Défense, ¨Paris.
On this occasion, Sylvie Retailleau, Minister for Higher Education and Research, announced the launch of a mission on the doctorate, entrusted to Sylvie Pommier and Xavier Lazarus, which will be supported by the ANRT.
Philippe Valet, Director of the “Cancer, Ageing and Rejuvenation” Graduate School was invited to present the work and organisation of this new transdisciplinary international education program.
See Philippe Valet intervention here. (2:36:41 – 3:46:30)

Insights into the disruption of gene regulatory programs in cancers – Workshop by Anthony Mathelier

On October 20 from 11 to 12, Dr Anthony Mathelier from the Molecular Medecine Norway Center will give a workshop at the Toulouse Research Center in Cancerology

Abstract:

Most cancer somatic alterations occur in the noncoding portion of the human genome, which contains important cis-regulatory regions acting as genetic switches to ensure gene expression occurs at correct times and intensities in correct tissues. However, the identification of critical noncoding cancer driver events has been mostly limited to a few examples with high recurrence or high functional impact. Transcription factors (TFs) are key proteins binding to cis-regulatory regions at their TF binding sites to modulate the rate of gene transcription. As cancer is a disease of disrupted cellular regulation, it is critical to analyze these regions to highlight patient somatic mutations and epigenetic modifications altering the gene regulatory program of the cells. In this talk, I will present our recent works on the interplay between TF binding, somatic mutations, and DNA methylation alteration that shifts the gene regulatory program in patients cancer cells.

If you are willing to attend this event online, please join here.

HUMAN GENE THERAPY: FROM BASIC PRINCIPLES TO APPLICATIONS IN THE MUSCULOSKELETAL SYSTEM

On Thursday, October 12th, at 9AM, Magali Cucchiarini, Professor of Molecular Biology & Vice-Director, Center of Experimental Orthopaedics at the Saarland University Medical Center is giving a workshop at RESTORE lab on human gene therapy.

Magali Cucchiarini, PhD, is a Professor, Group Leader, and Vice-Director of the Center of Experimental Orthopaedics, Saarland University Medical Center, Homburg/Saar, Germany, involved in the teaching activities of the Medical Faculty of the Saarland University (Biochemistry and Molecular Biolo-gy). She graduated from the University of Nice-Sophia Antipo-lis, France (PhD, summa cum laude), worked at the University Hospital Inselsspital, Bern Switzerland, and was a senior scientist at Harvard Medical School. Her research interest is to generate innovative cell-, gene-, and tissue engineered-based systems to treat musculoskeletal diseases.

If you want to join online, click here

1st Young Scientist Cancer Congress (YS2C) -New Research for cancer therapy- from bench to bedside

October 5th, 2023

The CRCT postdocs association was created in 2022 by Benoît Aliaga, Chloé Bessière and Steffen Fuchs. It gathers the 31 postdocs who are currently present in the Cancer Research Center of Toulouse. They decided to organize the 1st Young Scientist Cancer Congress of the Cancéropôle Grand Sud Ouest (GSO) on the 5th October 2023 at the Oncopole, Toulouse.

Aim: The main goals of this day are to promote the work of the GSO postdocs and young clinician scientists, to network, and to optimize their career paths.
Public: To achieve our goals, we decided to open the conference to the whole scientific community of the GSO, which are researchers and clinicians of all career levels.
Organization: This day will alternate presentations by internationally renowned keynote speakers, presentations by postdocs from the GSO, an application-focused presentation by a leading single-cell sequencing company and a presentation from an editor of Nature Communications about scientific publishing and peer-reviewing.

Lifelong orchestration of animal physiology by the circadian clock

On Thursday, September 21st, at 1PM, Frédéric Gachon, Associate Professor at the University of Queensland is giving a workshop at the RESTORE lab on the circadian clock.

To improve their adaptation to the changing environment presents on Earth, organisms from bacteria to mammals have evolved a timing system that anticipates these changes. This endogenous timing system, called the circadian clock, orchestrates most aspects of physiology and behavior. The mammalian circadian clock is hierarchically organized. A central clock localized in the Suprachiasmatic Nucleus (SCN) of the hypothalamus is daily synchronized by the light via the retina-hypothalamus tract and coordinates the peripheral clocks localized in peripheral tissues. The SCN synchronizes most aspects of circadian physiology throughout the life and is required to keep phase coherence between the different peripheral organs. While new data shows that this circadian clock is disrupted in many human pathologies and during aging, the impact of this disruption on these conditions is it still unclear.

TEAMS

Professor Tatiana Vidaurre Rojas from UPCH nominated as Doctor Honoris Causa

On Monday, June 26th, the University of Toulouse III – Paul Sabatier nominated Professor Tatiana Vidaurre Rojas, from the Cayetano Heredia Peruvian University (UPCH), as Doctor Honoris Causa.

Created in 1918, this title is one of the most prestigious distinctions awarded by French universities to honor “personalities of foreign nationality for eminent services rendered to science, literature or the arts, to France or to the University”.

Five leading scientists received the diplomas and insignia handed over by Professor Jean-Marc Broto, President of the University of Toulouse III – Paul Sabatier: M. Robert F. Anderson, Professor of Oceanographic Chemistry and Marine Biogeochemistry, Ewing-Lamont Doherty Earth Observatory, Columbia University (USA); Ms. Ruth Durrer, Professor of Theoretical Physics, Department of Theoretical Physics, Faculty of Science, University of Geneva (Switzerland); Ms. Sandra Einloft, Dean of the Polytechnique School, Pontifical Catholic University of Rio Grande do Sul (Brazil); Ms. Isabelle Adolé Glitho, Honorary Dean of the Faculty of Science, Professor of Entomology, University of Lomé (Togo); and Ms. Tatiana Vidaurre Rojas.

Professor Bruno Ségui, Deputy Director of the CARe Graduate School, gave Ms. Vidaurre Rojas’ laudation.

Professor Tatiana Vidaurre Rojas teaches at Peru’s Cayetano Heredia University, where she leads the Master’s program on medical oncology. Since 2022, a Memorandum of Understanding links this program with the University of Toulouse III – Paul Sabatier and the CARe Graduate School.

Professor Tatiana Vidaurre Rojas holds a Master’s degree in Public Health and is a medical oncologist at the Peru’s National Cancer Institute (INEN), where she has played a key role in the fight against cancer in Peru and Latin America. As institutional head of INEN between 2012 and 2016, she designed and implemented the “Plan Esperanza”, a pioneering plan of cancer prevention and control in Peru, which that has served as a benchmark for other developing countries. She also founded the “Club de la Mama”, Peru’s leading association supporting patients and their families in their fight against womens’ cancers. She is currently President of the Peruvian Cancer Society, and as such, in 2021, she initiated the anti-cancer law enacted by the Peruvian Congress.

Professor Tatiana Vidaurre Rojas is the author of over 50 research articles in leading international journals. She leads several cancer research programs, notably concerning breast cancer in women from native Andean communities.