Portrait of Paul François

Paul François

Associate Academic Member
Full Professor, Université de Montréal, Department of Biochemistry and Molecular Medicine
Adjunct Professor, McGill University, Department of Physics
Research Topics
Computational Biology
Dynamical Systems
Information Theory
Machine Learning Theory
Google Scholar

Biography

Paul François is a full professor in the Department of Biochemistry and Molecular Medicine in the Faculty of Medicine, Université de Montréal, and an adjunct professor in the Department of Physics at McGill University.

François is a biophysicist whose research focuses on the application of computational methods (including machine learning) to evolution, embryonic development and immunology. He is an associate academic member of Mila – Quebec Artificial Intelligence Institute.

Past positions:

- Associate professor of physics, McGill University (2016–2023)

- Assistant professor of physics, McGill University (2010–2016)

Education and training:

- Postdoc, Siggia Lab, The Rockefeller University, U.S. (2005–2010)

- PhD in theoretical physics, Hakim Lab, École Normale Supérieure / Université Paris VII, France (2002–2005)

- MSc in theoretical physics, École Normale Supérieure / École Polytechnique, France (2001–2002)

- BEng, major in physics, École Polytechnique (1998–2001), Promotion X 98

Some awards:

- 2019 Rutherford Memorial Medal in Physics, Royal Society of Canada

- 2017 CAP Herzberg Medal, Canadian Association of Physicists

- 2015 McGill Principal’s Prize for Outstanding Emerging Researcher

- 2014 Simons Investigator in Mathematical Modeling of Living Systems

- 2007 Lavoisier Postdoctoral Fellowship (from France’s Ministry of Foreign Affairs)

- 2007 Prix Le Monde de la recherche universitaire (awarded by the French newspaper Le Monde)

Current Students

Qichen Huang
Master's Research - Université de Montréal
Philippe Martin
PhD - Université de Montréal
Principal supervisor :
Guy Wolf
Victoria Mochulska
PhD - McGill University

Publications

Abstract 6324: Antagonism-enforced braking system to enhance CAR T cell therapeutic specificity
Taisuke Kondo
François X. P. Bourassa
Sooraj R. Achar
Justyn DuSold
Pablo Cespedes
Madison Wahlsten
Audun Kvalvaag
Guillaume Gaud
Paul E. Love
Michael Dustin
Grégoire Altan-Bonnet
Paul François
Naomi Taylor
Chimeric Antigen Receptor (CAR) T cell immunotherapy represents a breakthrough in the treatment of hematological malignancies. However, the … (see more)rarity of cell surface protein targets that are specific to cancerous but not vital healthy tissue has hindered its broad application to solid tumor treatment. While new logic-gated CAR designs have shown reduced toxicity against healthy tissues, the generalizability of such approaches across tumors remains unclear. Here, we harness a universal characteristic of endogenous T cell receptors (TCRs), their ability to discriminate between self and non-self ligands through inhibition of response against self (weak) antigens, to develop a broadly applicable method of enhancing immunotherapeutic precision. We hypothesized that this discriminatory mechanism, known as antagonism, would apply across receptors, allowing for a transfer of specificity from TCRs onto CARs. We therefore systematically mapped out the responses of CAR T cells to joint TCR and CAR stimulations. We first engineered murine T cells with an ovalbumin-specific TCR to express a CAR targeting murine CD19 and discovered that the expression of a strong TCR antigen on CD19+ leukemia enhanced CAR T killing. Importantly though, the presence of a weak TCR antigen antagonized CAR T responses, assessed by in vitro multiplexed dynamic profiling as well as in vivo cytotoxicity. We developed a mathematical model based on cross-receptor inhibitory coupling that accurately predicted the extent of TCR/CAR antagonism across a wide range of immunological settings. This model was validated in a CD19+ B16 mouse melanoma model showing that TCR/CAR antagonism decreased the infiltration of a tumor-reactive T cell cluster, while TCR/CAR agonism enhanced infiltration of this T cell cluster. We then applied our quantitative knowledge of TCR/CAR crosstalk to design an Antagonism-Enforced Braking System (AEBS) for CAR T cell therapy. This was assessed in a model system using a CAR targeting the tyrosine-protein kinase erbB-2 (HER2) together with a hedgehog acyltransferase (HHAT) peptide-specific TCR that binds strongly to mutated tumor neoantigen while retaining weak affinity for the wild-type self-antigen on healthy tissue. We established a humanized in vivo model of CAR T function and found that AEBS CAR T cells maintained high anti-tumor activity against a human lung adenocarcinoma (PC9) but notably, their anti-tissue cytotoxicity against human bronchial epithelial cells (BEAS-2B) was minimized. AEBS CAR T cells therefore sharpen the discriminatory power of synthetic anti-tumor lymphocytes. Our work highlights a novel mechanism by which TCRs can enforce CAR T cell specificity, with practical implications for the rational design of future anti-leukemia immunotherapies. Citation Format: Taisuke Kondo, François X. Bourassa, Sooraj Achar, Justyn DuSold, Pablo Cespedes, Madison Wahlsten, Audun Kvalvaag, Guillaume Gaud, Paul Love, Michael Dustin, Gregoire Altan-Bonnet, Paul François, Naomi Taylor. Antagonism-enforced braking system to enhance CAR T cell therapeutic specificity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6324.
2024-03-22
Cancer Research (published)
doi.org
Harnessing TCR/CAR Antagonism to Enhance Immunotherapeutic Precision
Taisuke Kondo
François X. P. Bourassa
Sooraj R. Achar
Justyn DuSold
Pablo Cespedes
Madison Wahlsten
Audun Kvalvaag
Guillaume Gaud
Paul E. Love
Michael Dustin
Grégoire Altan-Bonnet
Paul François
Naomi Taylor
2023-11-28
Blood (published)
doi.org
CD3ζ ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides
Guillaume Gaud
Sooraj R. Achar
François X. P. Bourassa
John S. Davies
Teri Hatzihristidis
Seeyoung Choi
Taisuke Kondo
Selamawit Gossa
Jan Lee
Paul Juneau
Naomi Taylor
Christian S. Hinrichs
Dorian B. McGavern
Paul François
Grégoire Altan-Bonnet
Paul E. Love
2023-11-09
Nature Immunology (published)
doi.org
TCR/Chimeric Antigen Receptor (CAR) Cross-Antagonism to Fine-Tune CAR-T cell Immunotherapy
Grégoire Altan-Bonnet
Taisuke Kondo
François X. P. Bourassa
Sooraj R. Achar
Justyn DuSold
Pablo Cespedes
Madison Wahlsten
Guillaume Gaud
Paul E Love
Mike Dustin
Paul François
Naomi Taylor
Chimeric antigen receptor (CAR) T cells, are created by extracting T cells from a cancer patient, engineering them to express a CAR targetin… (see more)g a tumor specific molecule, then reintroducing them back into the patient. A patient’s T cells contain their own endogenous T cell receptors (TCRs) however, which could potentially interact with the exogenous CAR inserted into the cell. In this study, we examine how TCR and CAR signals interact upon CAR-T activation. We show that weak TCR stimulation can reduce (antagonize) or increase overall CAR-T response, both in vitro and in vivo, across multiple tumor models, in both mouse and human T cells. We further show that the behavior of these TCR/CAR interactions can be manipulated by changing various characteristics of the TCR, CAR, and associated ligands. While this behavior is complex, we show that it can be described by a single mathematical model based on the adaptive kinetic proofreading scheme of ligand discrimination. We conclude by presenting potential applications for cancer immunotherapy. Intramural Research Program of the National Cancer Institute
2023-05-01
Journal of Immunology (published)
doi.org
What did the T cell see? A deep-learning model of CD8+ T cell activation reveals sharp antigen discrimination at the single cell level
Madison Wahlsten
Amin Akhshi
Sooraj R. Achar
Anagha Yogam Krishnan
Paul François
Grégoire Altan-Bonnet
Immunotherapies such as checkpoint blockade antibodies to block T cell exhaustion have been successful in several cancers such as non-small … (see more)cell lung cancer and melanoma, but limited in others (e.g., pancreatic or prostate carcinomas) owing to differences in tumor antigenicity. Therefore, quantifying tumor antigenicity is critical for successful immunotherapies. Our lab has shown that antigenicity can be encoded in a single parameter derived from bulk cytokine dynamics in ex vivo co-cultures between antigen presenting cells (APCs) and T cells. Here we built a model that can capture the antigenicity seen by individual cells. Using a custom robotic platform, we generated high-throughput kinetics of T cell activation in co-culture with APCs by analyzing cells at various timepoints across a large set of activation conditions. We performed spectral flow cytometry to measure the expression of up to 30 surface markers and intracellular signals per cell. To analyze our content-rich datasets, we designed a machine learning-based model that can classify the antigen seen by an individual cell using expression values from flow cytometry. The model performs well not only at classifying T cells (ROC-AUC > 0.91), but also APCs (ROC-AUC > 0.88), suggesting that each individual leukocyte may register the quality of antigen being presented. Blocking cytokine signaling disrupted this antigen classification. Our study demonstrates that every individual lymphocyte can bridge local and global response to achieve high discriminatory power of antigens.
2023-05-01
Journal of Immunology (published)
doi.org
New wave theory
Paul François
2023-02-15
Development (published)
doi.org
Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures
Felix Proulx-Giraldeau
Jan M Skotheim
Paul François
Cell size is controlled to be within a specific range to support physiological function. To control their size, cells use diverse mechanisms… (see more) ranging from ‘sizers’, in which differences in cell size are compensated for in a single cell division cycle, to ‘adders’, in which a constant amount of cell growth occurs in each cell cycle. This diversity raises the question why a particular cell would implement one rather than another mechanism? To address this question, we performed a series of simulations evolving cell size control networks. The size control mechanism that evolved was influenced by both cell cycle structure and specific selection pressures. Moreover, evolved networks recapitulated known size control properties of naturally occurring networks. If the mechanism is based on a G1 size control and an S/G2/M timer, as found for budding yeast and some human cells, adders likely evolve. But, if the G1 phase is significantly longer than the S/G2/M phase, as is often the case in mammalian cells in vivo, sizers become more likely. Sizers also evolve when the cell cycle structure is inverted so that G1 is a timer, while S/G2/M performs size control, as is the case for the fission yeast S. pombe. For some size control networks, cell size consistently decreases in each cycle until a burst of cell cycle inhibitor drives an extended G1 phase much like the cell division cycle of the green algae Chlamydomonas. That these size control networks evolved such self-organized criticality shows how the evolution of complex systems can drive the emergence of critical processes.
2022-09-30
eLife (published)
doi.org
Universal antigen encoding of T cell activation from high-dimensional cytokine dynamics
Sooraj R. Achar
François X. P. Bourassa
Thomas J. Rademaker
Angela Lee
Taisuke Kondo
Emanuel Salazar-Cavazos
John S. Davies
Naomi Taylor
Paul François
Grégoire Altan-Bonnet
2022-05-20
Science (published)
doi.org
Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures
Felix Proulx-Giraldeau
J. Skotheim
Paul François
Cell size is controlled to be within a specific range to support physiological function. To control their size, cells use diverse mechanisms… (see more) ranging from ‘sizers’, in which differences in cell size are compensated for in a single cell division cycle, to ‘adders’, in which a constant amount of cell growth occurs in each cell cycle. This diversity raises the question why a particular cell would implement one rather than another mechanism? To address this question, we performed a series of simulations evolving cell size control networks. The size control mechanism that evolved was influenced by both cell cycle structure and specific selection pressures. Moreover, evolved networks recapitulated known size control properties of naturally occurring networks. If the mechanism is based on a G1 size control and an S/G2/M timer, as found for budding yeast and some human cells, adders likely evolve. But, if the G1 phase is significantly longer than the S/G2/M phase, as is often the case in mammalian cells in vivo, sizers become more likely. Sizers also evolve when the cell cycle structure is inverted so that G1 is a timer, while S/G2/M performs size control, as is the case for the fission yeast S. pombe. For some size control networks, cell size consistently decreases in each cycle until a burst of cell cycle inhibitor drives an extended G1 phase much like the cell division cycle of the green algae Chlamydomonas. That these size control networks evolved such self-organized criticality shows how the evolution of complex systems can drive the emergence of critical processes.
2022-04-14
bioRxiv (preprint)
doi.org
Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling
Louis-Philippe Bergeron-Sandoval
Sandeep Kumar
Hossein Khadivi Heris
Catherine L. A. Chang
Caitlin E. Cornell
Sarah L. Keller
Paul François
Adam G. Hendricks
Allen J. Ehrlicher
Rohit V. Pappu
Stephen W. Michnick
Significance The uptake of molecules into cells, known as endocytosis, requires membrane invagination and the formation of vesicles. A versi… (see more)on of endocytosis that is independent of actin polymerization is aided by the assembly of membraneless biomolecular condensates at the site of membrane invagination. Here, we show that endocytic condensates are viscoelastic bodies that concentrate key proteins with prion-like domains to enable membrane remodeling. A distinct molecular grammar, namely the preference for glutamine versus asparagine residues, underlies the cohesive interactions that give rise to endocytic condensates. We incorporate material properties inferred using active rheology into a mechanical model to explain how cohesive interactions within condensates and interfacial tensions among condensates, membranes, and the cytosol can drive membrane invagination to initiate endocyosis. Membrane invagination and vesicle formation are key steps in endocytosis and cellular trafficking. Here, we show that endocytic coat proteins with prion-like domains (PLDs) form hemispherical puncta in the budding yeast, Saccharomyces cerevisiae. These puncta have the hallmarks of biomolecular condensates and organize proteins at the membrane for actin-dependent endocytosis. They also enable membrane remodeling to drive actin-independent endocytosis. The puncta, which we refer to as endocytic condensates, form and dissolve reversibly in response to changes in temperature and solution conditions. We find that endocytic condensates are organized around dynamic protein–protein interaction networks, which involve interactions among PLDs with high glutamine contents. The endocytic coat protein Sla1 is at the hub of the protein–protein interaction network. Using active rheology, we inferred the material properties of endocytic condensates. These experiments show that endocytic condensates are akin to viscoelastic materials. We use these characterizations to estimate the interfacial tension between endocytic condensates and their surroundings. We then adapt the physics of contact mechanics, specifically modifications of Hertz theory, to develop a quantitative framework for describing how interfacial tensions among condensates, the membrane, and the cytosol can deform the plasma membrane to enable actin-independent endocytosis.
2021-12-09
Proceedings of the National Academy of Sciences of the United States of America (published)
doi.org