NCube/papyrus huggingface dataset:
Nouvelles approches thérapeutiques pour prévenir les rechutes du neuroblastome : étude préclinique et translationnelle

Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. Despite aggressive multimodal therapy, 40% of patients with high-risk NB relapse. The current therapy comprises an induction treatment with chemotherapy and surgery, a consolidation treatment including radiotherapy and high-dose chemotherapy followed by bone marrow rescue with autologous hematopoietic stem cell transplantation and finally anti-GD2 immunotherapy targeting the disialoganglioside (GD2) antigen expressed by neuroblasts to treat minimal residual disease (MRD). Our preclinical study proposes two treatment strategies to potentiate current therapies and reduced toxicities. The first aim to reduce tumor mass by targeted radiotherapy combined with radiosensitizers. The second approach is based on the activation of natural killer (NK) cells to potentiate the effect of anti-GD2 therapy and eliminate MRD. Autophagy is a catabolic process that recycle damaged proteins and organelles, induced under various conditions of cellular stress including irradiation. Therefore, inhibiting autophagy could sensitize neuroblasts to irradiation. However, our study showed that neuroblasts were highly sensitive to irradiation and autophagy inhibitor failed to increase neuroblasts sensitization to irradiation. In addition, the absence of a potent autophagy inhibitor for therapeutic use does not allow this approach to be adopted.  Our preclinical study demonstrated a novel approach based on NK cell stimulation with Toll-like activated plasmacytoid dendritic cells (pDC) that enhances the efficacy of anti-GD2 immunotherapy and prevent NB relapse. We elucidated the mechanisms involved in pDC-activated NK cells killing of neuroblasts. We further demonstrated that neuroblasts were efficiently killed by patient’s NK cells after stimulation by activated pDC. This is further increased by the addition of anti-GD2 antibody. Altogether, our study demonstrates that NK cell-based immunotherapy has a real potential to enhance anti-GD2 immunotherapy effect and prevent NB relapse. This preclinical study will serve as a basis for the development of a clinical trial to treat children with NB at CHU Sainte Justine.

Keyphrases: Neuroblastoma, Autophagy, anti-GD2 immunotherapy, Natural killer cells, Plasmacytoid dendritic cells, Cancer immunotherapy
Studying biological assembly of ion channel complexes

Ion channels are key macromolecular complexes expressed in all cell types and are involved in various physiological processes including the generation and propagation of action potentials. Defective channels lead to severe diseases including epilepsy, arrhythmias and pain syndromes making them an interesting potential drug target. To improve our understanding of these biological assemblies and eventually find specific treatments for channelopathies, it is crucial to study the structure and function of ion channels. The main purpose of this thesis has been to investigate such structural and functional details of three ion channel complexes from the field of pain sensors and voltage-gated potassium channels using fluorescence and electrophysiological techniques. In the first project, we studied the stoichiometry of heteromeric Kv2.1/6.4 channel complexes (chapter three). Single subunit counting (SSC) allows to directly count the number of fluorescently labeled subunits by determining the number of irreversible, step-wise photobleaching events. To determine the most probable stoichiometry, we used weighted likelihood calculations and found that Kv2.1/6.4 channels express in a 2:2 arrangement. More precisely, functional studies of concatemeric channels (performed by our collaborators) illustrate that Kv6.4 and 2.1 subunits need to be arranged in an alternating fashion. The second project was also based on SSC experiments and aimed at determining the oligomeric state of the novel ion channel TACAN (chapter four). We found a significant amount of channels in the intracellular which caused background fluorescence in traditional SSC experiments performed in cells. To improve the signal to background ratio, we performed SSC experiments on purified channels that were immobilized on Ni-NTA functionalized glass coverslips. Using the model selection method described in the first project, we found different oligomeric states and propose that native TACAN channels assemble as tetramers which are unstable when solubilized in detergent. In the last project, we investigated the structure-function relation of the auxiliary DPP6 subunit in Kv4.2 channel complexes (chapter five). Here, we progressively truncated DPP6’s 700 amino acids long extracellular domain and studied its effect on macroscopic currents using the cut-open voltage clamp technique. We found that DPP6 subunits with a short extracellular domain fail to modulate the channel properties as efficiently as the full length DPP6. More precisely, the second half of the extracellular b-propeller domain of DPP6 is responsible for drastically accelerated channel inactivation. Based on the crystal structure of the extracellular domain, we proposed that a stable b-propeller domain and possibly DPP6 dimer formation is responsible for destabilizing the open channel state efficiently.

Keyphrases: Ion channels, Kv2.1/Kv6.4, TACAN, Kv4.2, DPP6, Single subunit counting, Cut-open oocyte voltage clamp, Voltage-clamp fluorometry
Rôle des Arfs et de leurs régulateurs dans la migration des cellules de bordure chez la drosophile

Cell migration is implicated in various important biological processes, notably it is central for the dissemination of cancer cells. Vesicular trafficking is a key regulator of cell migration, notably by controlling the localisation of proteins involved in migration such as integrins, cadherins and transmembrane receptors. In particular, our laboratory has shown that endocytosis controls orientation and cellular communication during collective cell migration. Our hypothesis is that other events of vesicular trafficking might be implicated in collective cell migration. Thus, the purpose of this thesis was to assess the function of small GTPases Arf, important for vesicle formation and cargo sorting into those vesicles, and their regulators in collective cell migration. A powerful model to study collective cell migration is the migration of follicular cells named border cells during oogenesis in Drosophila melanogaster. Border cells (BCs) detach from the follicle epithelium surrounding the egg chambers and form a small cluster of six to ten cells that migrates invasively between the giant nurse cells that compose the center of the egg chamber, toward the oocyte. Accordingly to our hypothesis, a strong migration defect is observed when the Arfs are depleted specifically in the border cells. Moreover, a similar finding is observed after depletion of some Arfs regulators (ArfGAPs and ArfGEFs). In particular, the ArfGAP Drongo and its GTPase-activating function are essential for the initial detachment of the border cell cluster from the basal lamina. We demonstrated through protein localization and genetic interactions that Drongo controls the localisation of the myosin phosphatase in order to regulate myosin II activity at the back of the cluster and promote border cells detachment. Moreover, we showed that Drongo acts on the class III Arf (Arf51F) antagonistically to the guanine exchange factor Steppke to displace myosin phosphatase from the back of the cluster. On the other hand, we have also demonstrated that the GAP ArfGAP1 controls the directionality of migration. This ArfGAP potentially acts by regulating the localization of certain determinants of migration such as E-cadherin and receptors tyrosine kinase. Thus, our research has demonstrated an essential role for Arfs in collective cell migration and specific contributions of two ArfGAPs in this migration process.

Keyphrases: GTPases Arf, ArfGAPs, Drongo, ArfGAP1, Drosophile, Cell migration, Vesicular trafficking, Arf GTPases, Border cells, Drosophila
Use of chemogenomic approaches to characterize RUNX1-mutated Acute Myeloid Leukemia and dissect sensitivity to glucocorticoids

RUNX1 is an essential transcription factor for definite hematopoiesis and plays important roles in immune function. Mutations in RUNX1 occur in 5-13% of Acute Myeloid Leukemia (AML) patients (RUNX1mut ) and are associated with adverse outcome, thus highlighting the need for better genetic characterization and for the design of efficient therapeutic strategies for this particular AML subgroup. Although most RUNX1 mutations in AML are believed to be acquired, germline RUNX1 mutations are observed in the familial platelet disorder with predisposition to hematologic malignancies (RUNX1-FPD, FPD/AML) in which about 44% of affected individuals progress to AML. By performing RNA-sequencing of the Leucegene collection, we revealed that RUNX1 allele dosage influences the association with cooperating mutations, gene expression profile, and drug sensitivity in RUNX1mut primary AML specimens. Validation of RUNX1 mutations led to the discovery that 30% of RUNX1 mutations in our AML cohort are of germline origin, indicating a greater than expected proportion of cases with familial RUNX1 mutations. Chemical screening showed that most RUNX1mut specimens are sensitive to glucocorticoids (GC) and we confirmed that GCs inhibit AML cell proliferation via interaction with the Glucocorticoid Receptor (GR). We observed that specimens harboring RUNX1 mutations expected to result in low residual RUNX1 activity were most sensitive to GCs, and that co-associating mutations, such as SRSF2mut, as well as GR levels contribute to GC-sensitivity. Accordingly, acquired GC-sensitivity was achieved by negatively regulating RUNX1 expression in human AML cells, which was accompanied by upregulation of the GR. GC-induced transcriptome analysis revealed that GC-induced differentiation of AML cells might be a mechanism at play in the antiproliferative response to these drugs. Most critically, functional genomic screening identified the transcriptional repressor PLZF (ZBTB16) as a specific modulator of the GC response in sensitive and resistant AML cells. These findings provide additional characterization of RUNX1mut AML, further stressing the importance of germline testing for patients carrying deleterious RUNX1 mutations. Our results also identified a novel role for RUNX1 in the GR signaling network and support the rationale of investigating GC repurposing for RUNX1mut AML in preclinical models. Finally, we provided insights into the mechanism of action of GCs, which positions PLZF as an important factor promoting resistance to glucocorticoids in AML.

Keyphrases: Acute Myeloid Leukemia, RUNX1, Glucocorticoids, Chemogenomics, CRISPR-Cas9 screening, Glucocorticoid-resistance, criblage CRISPR-Cas9
The roles of protein phosphatase 2A in nuclear envelope reformation after mitosis in drosophila

During nuclear envelope breakdown, the cyclin-dependent kinase 1 bound to Cyclin B (CDK1-Cyclin B) and other kinases phosphorylate a number of nuclear proteins leading to the disassembly of nuclear envelope protein complexes. Phosphorylated nuclear proteins are then dephosphorylated by a group of phosphatases at mitotic exit. The protein phosphatase 2A in complex with the regulatory subunit B55 (PP2A-B55) is known to be the major phosphatase to dephosphorylate critical proteins at the end of mitosis. However, little was known about the nuclear substrates dephosphorylated by PP2A-B55 at mitotic exit. Using Drosophila cells in culture, we demonstrated that PP2A-B55 is required for the recruitment of nuclear envelope proteins such as BAF, the nuclear lamina protein Lamin B, and the nucleoporin Nup107. Also, eggs from Drosophila females heterozygous for a mutation in genes coding for Lamin B and Tws (B55 in Drosophila), didn’t hatch. These eggs showed various defects during the nuclear division stage and meiosis. Moreover, in vitro assays and other biochemical analyses indicate that PP2A-B55 binds and dephosphorylates BAF. I have other results that suggest a role of the protein Ankle2 in regulating BAF recruitment to reassembling nuclei at mitotic exit. My results also suggest that Ankle2 in complex with PP2A is responsible for the proper mitotic progression. Our results highlight the importance of Drosophila in investigating different aspects of the cell cycle. It also demonstrates a role of PP2A in the nuclear envelope reformation at the end of mitosis.

Keyphrases: PP2A-B55, Ankle2, Nuclear envelope reformation, Drosophila, Mitosis
BMI1 mediated heterochromatin compaction represses G-quadruplex formation in Alzheimer's disease

Alzheimer's disease is the most prominent dementia in the developed world. This neurodegenerative disease renders the ability to do the routine daily tasks more and more difficult; it can also cause patients to forget words, be disoriented in time and space, leading to a memory loss. Unfortunately, AD is considered the next big challenge for most country’s public health, with the number of cases thought to be doubling within the next 20 years due to the aging of the population. This increase in the number of patients comes with an increase in the need for funding and for healthcare personnel to meet the demands and the requirements of these patients. AD is divided into two separate entities: a well-defined and understood hereditary disease that makes up to 5% of all AD cases called familial Alzheimer disease, and a less defined one called sporadic Alzheimer disease. sAD most defined risk factor is age, but recently it was shown that brains of sAD patients had a reduced level of BMI1 and that the knockdown of BMI1 in human neurons or mice triggers the hallmarks of this disease. While BMI1 was known to be important in the developmental stages, we report here that it is crucial in adult cells to maintain the compaction of the chromatin and the silencing of the repetitive sequences. Furthermore, these two functions of BMI1 prevent the DNA from acquiring a G4 conformation. This conformation can lead to genome instability, increased DNA damage, and altered gene expression. However, most importantly, we showed that in cortical neurons, G4 structures could influence the alternative splicing of various genes, notably APP. These results shed new light on the origin of AD, and the importance of BMI1 and the secondary structure of the DNA in its context.

Keyphrases: BMI1, G4, Alzheimer’s disease, polycomb, LINE sequences, genome instability
Essays in functional econometrics and financial markets

In this thesis, I exploit the functional data analysis framework and develop inference, prediction and forecasting analysis, with an application to topics in the financial market. This thesis is organized in three chapters. The first chapter is a paper co-authored with Marine Carrasco. In this chapter, we consider a functional linear regression model with a functional predictor variable and a scalar response. We develop a theoretical comparison of the Functional Principal Component Analysis (FPCA) and Functional Partial Least Squares (FPLS) techniques. We derive the convergence rate of the Mean Squared Error (MSE) for these methods. We show that this rate of convergence is sharp. We also find that the regularization bias of the FPLS method is smaller than the one of FPCA, while its estimation error tends to be larger than that of FPCA. Additionally, we show that FPLS outperforms FPCA in terms of prediction accuracy with a fewer number of components. The second chapter considers a fully functional autoregressive model (FAR) to forecast the next day’s return curve of the S&P 500. In contrast to the standard AR(1) model where each observation is a scalar, in this research each daily return curve is a collection of 390 points and is considered as one observation. I conduct a comparative analysis of four big data techniques including Functional Tikhonov method (FT), Functional Landweber-Fridman technique (FLF), Functional spectral-cut off (FSC), and Functional Partial Least Squares (FPLS). The convergence rate, asymptotic distribution, and a test-based strategy to select the lag number are provided. Simulations and real data show that FPLS method tends to outperform the other in terms of estimation accuracy while all the considered methods display almost the same predictive performance. The third chapter proposes to estimate the risk neutral density (RND) for options pricing with a functional linear model. The benefit of this approach is that it exploits directly the fundamental arbitrage-free equation and it is possible to avoid any additional density parametrization. The estimation problem leads to an inverse problem and the functional Landweber-Fridman (FLF) technique is used to overcome this issue.

Keyphrases: Big data, Landweber-Fridman, Tikhonov, Estimation, S&P 500, Options, Functional regression, Functional data analysis, Functional Autoregressive model, Functional principal component, Functional partial least squares, Forecasting, Risk neutral density, Financial markets
Essays in innovation, inequality and risk

This thesis is organized into three chapters in the economics of innovation and science. In doing so, it develops empirical and theoretical models to analyze technological and scientific innovation and produce policy recommendations. The first chapter uses data science and big data techniques to build an indicator of technological innovation. Using a unique database on patents in Canada, we build a patent quality index to answer two main questions: the absence of a systematic database on patents and their value in Canada and the evaluation of the pharmaceutical sector, one of the leading innovating sectors in Canada. The results reveal that our quality index is linked to the economic performance of firms, their productivity, and aggregate productivity. The second chapter looks at innovations in academic research. Specifically, focusing on economics, this chapter aims to connect innovation and inequality by analyzing the recognition of women's ideas in the field. Bibliometric data from research in economics are used to investigate gender biases in citation patterns. Based on deep learning and machine learning techniques, one can (1) establish the similarities between papers (2) build a link between articles by identifying the papers citing, cited and that should be cited. This study finds that, on average, omitted papers are 20% more likely to be female-authored than male-authored. This omission bias is more prevalent when there are only males in the citing paper. Overall, to have the same level of citation as papers written by males, papers written by females need to be 20 percentiles upper in the distribution of the degree of innovativeness of the paper. Finally, the last chapter analyzes innovation from a more macroeconomic perspective, focusing on entrepreneurs. Indeed, entrepreneurs are at the core of economic development and innovation. However, entrepreneurship remains very risky. What are the opportunities for investment risk diversification for entrepreneurs? To answer this question, we investigate the role of financial integration. With a theoretical model featuring a continuous-time dimension with heterogeneous agents, we show that financial openness produces substantial welfare gains for entrepreneurs and therefore can help its agents to diversify the investment risk. Our results are also supported by empirical analysis.

Keyphrases: Innovation, Entrepreneuriat, Economic Fluctuations and Growth, Entrepreneurship, Gender Inequality, Academic Research
La recherche sur le transfert des connaissances pour améliorer le dépistage et le traitement des troubles du comportement alimentaire

Despite considerable recent advances in the field of eating disorders (ED) prevention and intervention, access to quality care is limited because: 1) stigma associated with certain ED characteristics can lead to EDs’ going undiagnosed and untreated; 2) healthcare professionals do not always apply available evidence-based practices; and 3) given that knowledge on evidence-based practices is currently disseminated primarily in graduate programs, there are not enough clinicians trained in ED intervention. Thus, the study of knowledge transfer (KT) is vital to facilitate uptake of evidence-based practices by healthcare professionals. The aim of the present thesis is to better understand the research–practice gap in the field of ED with a view to improving access to evidence-based treatment. More specifically, the aim of this thesis is to document outcomes of KT strategies (e.g. educational materials, clinical guidelines, training workshops, supervision) and conditions influencing healthcare professionals’ evidence-based practices. Potential applications for Quebec’s intervention context are also of interest. The thesis consists of two articles and a discussion of main results. The first article documents, in a systematic review, the effects of available KT strategies and conditions influencing evidence-based practices of healthcare professionals and ED treatment teams. The findings suggest a combination of KT strategies might facilitate access to care. Articles reporting conditions that might support decision-making or interdisciplinary work were rare. In light of known challenges in ED intervention and the findings of this review, recommendations are presented to improve evidence uptake. The second article evaluates the impact of a training workshop on ED screening and referral practices by healthcare providers in Quebec’s first-line services. Results indicate that healthcare professionals used evidence- based knowledge in diverse ways (instrumental, conceptual and persuasive use) and under different conditions. This thesis furthers knowledge by identifying relevant strategies for facilitating healthcare professionals’ uptake of evidence-based practices throughout their decision-making processes.

Keyphrases: Knowledge transfer, Evidence-based practice, Evaluation use, Interdisciplinary teams, Eating disorders