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Intratumoural heterogeneity complicates the molecular interpretation of biopsies, as multiple distinct tumour genomes are sampled and analysed at once. Ignoring the presence of these populations can lead to erroneous conclusions, and so a correct analysis must account for the clonal structure of the sample. Several methods to reconstruct tumour clonality from sequencing data have been proposed, spanning methods that either do not consider phylogenetic constraints or posit a perfect phylogeny. Models of the first type are typically latent feature models that can describe the observed data flexibly, but whose results may not be reconcilable with a phylogeny. The second type, instead, generally comprises non-parametric mixture models, with strict assumptions on the tumour’s evolutionary process. The focus of this dissertation is on the development of a phylogenetic latent feature model that can bridge the advantages of these two approaches, allowing deviations from a perfect phylogeny. The work is recounted by three statistical models of increasing complexity. First, I present a non-parametric model based on the Indian Buffet Process prior, and highlight the need for phylogenetic constraints. Second, I develop a finite, phylogenetic extension of the previous model, and show that it can outperform competing methods. Third, I generalise the phylogenetic model to arbitrary copy-number states. Markov chain Monte Carlo algorithms are presented to perform inference. The models are tested on datasets that include synthetic data, controlled biological data, and clinical data. In particular, the copy-number generalisation is applied to longitudinal circulating tumour DNA samples. Liquid biopsies that leverage circulating tumour DNA require sensitive techniques in order to detect mutations at low allele fractions. One method that allows sensitive mutation calling is the amplicon sequencing strategy TAm-Seq. I present bioinformatic tools to improve both the development of TAm-Seq amplicon panels and the analysis of its sequencing data. Finally, an enhancement of this method is presented and shown to detect mutations de novo and in a multiplexed manner at allele fractions less than 0.1%.

Understanding the mechanisms and nature of tumour heterogeneity is a key focus of current cancer research. Tumour heterogeneity can arise from clonal evolution and/or differentiation. This thesis investigated the role of methylation in dynamic regulation of CD24 based heterogeneity in colorectal cancer cell lines. First, E-Cadherin variation between the cell lines LS174T and LS180 was investigated to find out whether E-Cadherin had any causal role in the difference in lumen formation between these two cell lines derived from the same tumour. These studies found no evidence of a causal role of E-Cadherin. However, morphological heterogeneity in LS174T was observed during the E-Cadherin study, suggesting that this cell line might be a mixture of two different clones. Single cell sorting by FACS allowed to isolate and establish these clones which were stable in the culture for long enough (until passage ~30) to allow their characterisations. Between the two clones, the CD24⁺ clone (named the LS174T_Clone 1^CD24+) was found to have shorter doubling time (23 hours) than the CD24- clone (named the LS174T_Clone 2CD24-; 30 hours). When cultured in matrigel, the LS174T_Clone 1^CD24+ showed higher clonogenicity (Chapter 4). Microarray analysis further revealed differences in gene expression including LAPTM4B, CXCR4, TGFIB and IL8 between these clones. Interestingly, when maintained for a long time in culture (around passage 50, which is equivalent to ~7 months), CD24 expression went through a gradual change in these clones, which became more evident from subclones of LS174T_Clone 2^CD24- (Chapter 6) and clones from another CRC cell line SW480 (chapter 5 and 6). To understand the mechanism of this dynamic change in the expression of CD24, it was first shown that no mutation could be responsible for this phenomenon. This suggested that promoter methylation of CD24 might be the mechanism of the observed dynamic changes in CD24 expression. Bisulfite (BS) modification of DNA from the LS174T clones and CD24 differentially expressing CRC cell lines (such as CD24- cell lines: CC20, RKO vs CD24+ cell lines: DLD1, NCIH716) followed by Sanger sequencing showed that direct methylation of seven CpG positions in the CD24 promoter region Chr6:106975560-106975834 is strongly correlated with the expression of CD24. Further subcloning and sequencing revealed that changes in the methylation of only two out of the seven CpG positions might be the main contributor to the CD24 expression differences. This is the first evidence of direct methylation-mediated regulation of CD24, showing, more broadly, how methylation can contribute to and maintain dynamic heterogeneity in cancer cells. Finally, a mixed culture experiment with the CD24+ and CD24- clones was conducted to test a simple mathematical model, which aimed to explain the interaction between the clones that are stably present in the LS174T cell line (Chapter 7). Altogether, these experiments suggest that genes such as REG1A (an inducer of angiogenesis) might be expressed because of synergistic interactions between the clones, whereas CXCR4 and TFF2 might be involved in a receptor-ligand complementary relationship. These findings have set a ground for future studies to confirm such interactions between co-existing subpopulations within a heterogeneous milieu of cancer cells.

Dans la première partie de cette thèse, nous étudierons l’impact de l’hétérogénéité tumorale sur les phénomènes d’invasion collective des cellules cancéreuses et de dissémination métastatique.L’hétérogénéité des populations cellulaires tumorales est observée dans la plupart des lésions cancéreuses solides. Cependant, son impact sur le phénomène de métastase – élément prépondérant dans l’établissement du pronostic vital du patient – demeure à ce jour mal compris. En utilisant un modèle numérique minimal de tumeur, nous avons cherché à déterminer quel était l’impact de l’hétérogénéité des propriétés mécaniques des cellules cancéreuses sur leur invasion dans les tissus sains entourant la tumeur. Nous nous sommes particulièrement intéressés aux différences de mobilité cellulaire au sein des diverses populations cellulaires composant une tumeur. Nos travaux établissent un lien de causalité entre l’hétérogénéité tumorale et la dissémination métastatique. De plus, ils permettent de reproduire un certain nombre de morphologie d’invasion cancéreuse telles que des protrusions pluricellulaires en forme de « doigts » ou d’agrégats. Nos expériences in silico démontrent que deux mécanismes complémentaires sont à l’œuvre au sein des tumeurs hétérogènes. Une faible proportion de cellules leaders, possédant une force mobile plus élevée, est capable d’initier et de diriger l’invasion cancéreuse, alors que les effets de mouvements collectifs au sein de la tumeur fournissent la coordination mécanique nécessaire à un phénomène d’invasion collectif continu. Ces résultats suggèrent que la dynamique d’invasion collective observée durant le processus de métastase est un phénomène universel. Celui-ci est propre aux populations de cellules aux propriétés mécaniques hétérogènes, et peut être décrit en se fondant sur un nombre limité d’hypothèses physiques, et ce malgré l’importante variabilité génétique et phénotypique qui caractérise les pathologies cancéreuses.Dans la seconde partie de cette thèse, nous continuerons à étudier l’impact de l’hétérogénéité des propriétés cellulaires, cette fois à l’échelle d’un organisme pluricellulaire et non pas seulement d’un tissu. Nous nous intéresserons au développement de l’amibe sociale Dictyostelium discoideum. Lorsque les amibes sont privées de nourriture, elles forment des agrégats pluricellulaires nommés slugs,dans lesquels les cellules initialement identiques se différencient et se ségrèguent en deux populations distinctes : les cellules prespores, à l’arrière, et les cellules prestalks, à l’avant. La formation de ce motif spatial est caractérisé par une homéostasie des proportions des types cellulaires, qui demeurent quasi constants malgré les variations importantes du nombre de cellules au sein des agrégats. Si différents modèles ont été proposés pour expliquer l’origine de ce phénomène, il demeurait nécessaire de mettre en place des expériences quantitatives afin de confirmer ou d’infirmer ces modèles. Dans ce but, nous avons développé et caractérisé une nouvelle souche cellulaire de Dictyostelium, AX2-PYR, utilisant des sondes fluorescentes génétiquement encodées permettant de distinguer les différents types cellulaires au sein des slugs. Nos résultats démontrent l’invariance du motif prespore/prestalk avec la taille des slugs sur quatre ordres de grandeur, et mettent en évidence l’existence d’un mécanisme actif de régulation des proportions reposant sur les communications intercellulaires. / In the first part of this thesis, we study the impact of tumour heterogeneity on cancer collective invasion and metastatic dissemination. Heterogeneity within tumour cell populations is commonly observed in most solid tumours, but its impact on metastasis, one of the primary determinants of the disease prognosis, remains poorly understood.Working with a simplified numerical model of tumour spheroids, weinvestigate the impact of mechanical heterogeneity of tumour cells on the onset of tumour invasion into surrounding tissues, focusing more particularly on the influence of differences in cell motility. Ourwork establishes a positive link between tumour heterogeneity and metastatic dissemination, and recapitulates a number of invasion patterns identified in vivo, such as multicellular finger-like protrusionsor tumour cell clusters. In our in silico experiments, we demonstrate that two complementary mechanisms are at play in heterogeneous tumours: a small proportion of stronger cells with a higher motile force are able to initiate and lead the escape from the tumour, while collective effects in the bulk of the tumour provide the coordination required to sustain the invasive process through multicellular streaming. This suggests that the multicellular dynamics observed during metastasis is a generic feature of mechanically heterogeneous cell populations and might rely on a limited and generic set of physical assumptions shared by most tumours in spite of the genetic and phenotypic variability amongst patients and pathologies.In the second part of our work, we continue to explore the impact of heterogeneity on population scale behaviours of multicellular systems, focusing on the development of the social amoeba Dictyosteliumdiscoideum. Under starvation Dictyostelium cells form multicellular aggregates named slugs where amoeba cells differentiate and segregate into two distinct spatial zones, the prespore (rear) and prestalk (front) cells regions. This developmental pattern is characterized by an homeostasis of cell-type proportions with respect to slug size and external perturbations. Different models have been proposed to explain theorigin and regulation of this pattern, but quantitative experiments were still needed to decipher between the proposed mechanisms. To quantitatively investigate cell differentiation and spatial patterning in live multicellular aggregates, we developed and characterized a new stable cell line, AX2-PYR, using genetically encoded fluorescent reporters of cell differentiation into prespore and prestalk cells. Our results demonstrate the scaling of the prespore/prestalk pattern over more than three orders of magnitude in slug size, and show the existence of a proportion regulation mechanism which might rely on cell-cell communications.

Carbonic anhydrase IX (CA9) is strongly induced by hypoxia and its overexpression is associated with poor therapeutic outcome in cancer. The function of CAIX is to catalyze the reversible hydration of CO2 to bicarbonate and a proton. This helps hypoxic tumours to maintain a more neutral intracellular pH (pH_i) promoting survival, but produces a more acidic extracellular (pH_e) which promotes invasion and metastasis. Recent evidence has expanded on the role of hypoxia and CAIX by relating them to stem cell niches. In this study, taking advantage of the transmembrane location of CAIX, we show for the first time, a direct marked heterogeneity in response to hypoxia within each tumour cell population studied, associated with major biological differences. Based on CAIX expression pattern under hypoxic conditions, we identify, isolate and characterize two distinct populations of tumour cells, one that express CAIX and the other that does not. Interestingly, we discover that the CAIX positive population is enriched with cells expressing cancer stem cell markers. These include ALDHA1, IGF1, LIN28 and genes involved in epithelial-mesenchymal transition (EMT) and multi-drug resistance (i.e. WNT2, TWIST1, and ABCC2). Accordingly, CAIX+ve cells show higher self-renewal capacity and form tumours significantly faster compared to the CAIX-ve population. Importantly, functional suppression of CAIX in vitro and in vivo, in two breast cancer cell lines resulted in the downregulation of breast cancer stem cell signatures, suggesting that CAIX is not just a marker of stemness but also a regulator of stemness. The molecular mechanism underlying the differential expression of CAIX in the two populations is not HIF-1α-dependent, but instead driven by hypoxia-induced reorganization of chromatin structure. In line with this, we provide experimental evidence showing that the genomic locus encoding CA9 has a more “open” and transcriptionally active chromatin structure in CAIX+ve cells, and a condense and transcriptionally silent chromatin structure in the CAIX-ve cells. Given that HIF induces the transcription of CA9 by binding to hypoxia response elements (HREs) in its promoter we show a significant reduction in binding of HIF to the CA9 promoter of the negative population. We suggest that the reduce HIF binding is a result of the compact chromatin structure of CA9 promoter of the negative cells. Analysis of the transcriptome of the positive and negative populations suggests a symbiotic relationship between these two subpopulations and their environment, likely required to promote tumour growth. This is based on the following observations: Firstly, we identified that CAIX-ve cells express high levels of cytokines and based on this, we suggest that the cytokines secreted by CAIX-ve cells may transmit paracrine signals that regulate the CAIX+ve cells, thus providing a wider hypoxia tolerant microenvironment to protect the stem cell population. Secondly, we identified a metabolic heterogeneity between the CAIX+ve and CAIX-ve cells. The CAIX+ve cells show an upregulation of genes implicated in oxidative phosphorylation, TCA cycle and fatty acid synthesis. Whereas in CAIX-ve cells there is an upregulation of genes implicated in autophagy and mitophagy. Given the above together with the upregulation of oxidative phosphorylation and TCA cycle in the CAIX+ve cells, we proposed the existence of a metabolic symbiosis between the CAIX+ve and CAIX-ve cells. We postulate that the catabolic process such as autophagy and mitophagy in the CAIX-ve cells may results in the overproduction of high-energy metabolites such as lactate, glutamine and ketone bodies which in turns they are been utilized by CAIX+ve cells to fuel mitochondria respiration. Finally, we also demonstrated that in the CAIX+ve cells mTORC1 signaling is upregulated, and contributes to the regulation of CAIX expression. Given the role of mTORC1 in stem cell maintenance and EMT as well as the interdependence of mTORC1 and CAIX expression in the CAIX+ve cells we suggest that mTORC1 signaling may be the critical factor by which CAIX regulates stemness. Interestingly, the subpopulations show a differential sensitivity to HDAC inhibitors, NaBu and SAHA as treatment of MCF7 breast cancer cell line and HCT116 colon cancer cell line leads to elimination of the CAIX+ve population. This is not driven by the downregulation of HIF-1α, the major transcriptional regulator of CAIX. In contrast, we demonstrate that SAHA causes downregulation mTORC1. This suggests that SAHA-induced downregulation of CAIX expression could be due to its effect on mTORC1 pathway. Of wider significance, our findings show that tumours are not homogenous in their response to hypoxia, and distinct signal transduction networks regulate different populations of cells within the tumour. This highlights the need for the utilization of biomarkers, which reveal distinct functional hypoxia profiles of human cancers, and permit the stratification of tumours. Furthermore, the identification of epigenetic regulation of the histones in response to hypoxia for highly selective gene regulation, provides a connection between the epigenetic mechanisms under environmental stress and cancer progression, and is model for development of novel epigenetic cancer therapeutic drugs.

Cancer related mortality is almost always due to metastatic dissemination of the primary disease. While research into the biological mechanisms that drive the metastatic cascade continues to unravel its molecular underpinnings, progress in our understanding of biological phenomena such as tumour heterogeneity and its relevance to the origins of distant recurrence or the emergence of resistance to therapy has been limited.In parallel to major breakthroughs in the development of high throughput molecular techniques, researchers have begun to utilise next generation sequencing to explore the relationship between primary and matched metastatic tumours in diverse types of neoplasia. Despite small cohort sizes and often, a limited number of matched metastases for each patient, pioneering studies have uncovered hitherto unknown biological processes such as the occurrence of organ specific metastatic lineages, polyclonal seeding and homing of metastatic cells to the primary tumour bed. While yet other studies continue to highlight the potential of genomic analyses, at the time this thesis was started, an in-depth knowledge of disease progression and metastatic dissemination was currently lacking in breast cancers.Herein, we employed phylogenetic inference methods to investigate intra-tumour heterogeneity and evolution of breast cancers. A combination of whole exome sequencing, custom ultra-deep resequencing and copy number profiling were applied to primary tumours and their associated metastases from ten autopsied breast cancer patients. Two modes of metastatic progression were observed. In the majority of cases, all distant metastases clustered on a branch separate from their primary lesion. Clonal frequency analysis of somatic mutations showed that the metastases had a monoclonal origin and descended from a common metastatic precursor. Alternatively, the primary tumour was clustered alongside metastases with early branches leading to distant organs. This dichotomy coincided with the clinical history of the patients whereby multiple seeding events from the primary tumour alongside cascading metastasis-to-metastasis disseminations occurred in treatment naïve de novo metastatic patients, whereas descent from a common metastatic precursor was observed in patients who underwent primary surgery followed by systemic treatment. The data also showed that a distant metastasis can be horizontally cross-seeded and finally revealed a correlation between the extent of somatic point mutations private to the distant lesions and patient overall survival. In an unrelated dataset of relapsed breast cancer patients with matched primary and distant lesions profiled using whole genome sequencing, the landscape of somatic alterations confirmed the time dependency of copy number aberrations implying that cancer phylogenies can be dated using a molecular clock.The work presented here harnesses the strength of high throughput genomic techniques and state of the art phylogenetic tools to tell the evolutionary history of breast cancers. Our results show that the linear and parallel models of metastatic dissemination which have been held as near doctrines for many years are overstated point of views of cancer progression. Beyond the biological insights, these results suggest that surgical excision of the primary tumour in de novo metastatic breast cancers might reduce dissemination in selected cases hence providing a potential biological rationale for this practice. Similarly, there is no strong evidence of benefit in overall survival from surgical resection of oligo-metastases in breast cancer. From our analyses, metastatic lesions constitute an additional source of seeding and heterogeneity in advanced breast cancer. The data presented here is too small to derive practice-changing evidence, but supports the concept that resecting isolated metastases may be of clinical benefit in oligo-metastatic breast cancer patients. In both cases, results from larger prospective studies are warranted. / Doctorat en Sciences biomédicales et pharmaceutiques (Médecine) / info:eu-repo/semantics/nonPublished

The tumour microenvironment comprises the non-cancerous cells present in the tumour mass (fibroblasts, endothelial, and immune cells), as well as signalling molecules and extracellular matrix. Tumour growth, invasion, metastasis, and response to therapy are influenced by the tumour microenvironment. Therefore, characterising the cellular and molecular components of the tumour microenvironment, and understanding how they influence tumour progression, represent a crucial aim for the success of cancer therapies. High-grade serous ovarian cancer provides an excellent opportunity to systematically study the tumour microenvironment due to its clinical presentation of advanced disseminated disease and debulking surgery being standard of care. This thesis first presents a case report of a long-term survivor (>10 years) of metastatic high-grade serous ovarian cancer who exhibited concomitant regression/progression of the metastatic lesions (5 samples). We found that progressing metastases were characterized by immune cell exclusion, whereas regressing metastases were infiltrated by CD8+ and CD4+ T cells. Through a T cell - neoepitope challenge assay we demonstrated that pre- dicted neoepitopes were recognised by the CD8+ T cells obtained from blood drawn from the patient, suggesting that regressing tumours were subjected to immune attack. Immune excluded tumours presented a higher expression of immunosuppressive Wnt signalling, while infiltrated tumours showed a higher expression of the T cell chemoattractant CXCL9 and evidence of immunoediting. These findings suggest that multiple distinct tumour immune microenvironments can co-exist within a single individual and may explain in part the hetero- geneous fates of metastatic lesions often observed in the clinic post-therapy. Second, this thesis explores the prevalence of intra-patient tumour microenvironment het- erogeneity in high-grade serous ovarian cancer at diagnosis (38 samples from 8 patients), as well as the effect of chemotherapy on the tumour microenvironment (80 paired samples from 40 patients). Whole transcriptome analysis and image-based quantification of T cells from treatment-naive tumours revealed highly prevalent variability in immune signalling and distinct immune microenvironments co-existing within the same individuals at diagnosis. ConsensusTME, a method that generates consensus immune and stromal cell gene signatures by intersecting state-of-the-art deconvolution methods that predict immune cell populations using bulk RNA data was developed. ConsensusTME improved accuracy and sensitivity of T cell and leukocyte deconvolutions in ovarian cancer samples. As previously observed in the case report, Wnt signalling expression positively correlated with immune cell exclusion. To evaluate the effect of chemotherapy on the tumour microenvironment, we compared site-matched and site-unmatched tumours before and after neoadjuvant chemotherapy. Site- matched samples showed increased cytotoxic immune activation and oligoclonal expansion of T cells after chemotherapy, unlike site-unmatched samples where heterogeneity could not be accounted for. In addition, low levels of immune activation pre-chemotherapy were found to be correlated with immune activation upon chemotherapy treatment. These results cor- roborate that the tumour-immune interface in advanced high-grade serous ovarian cancer is intrinsically heterogeneous, and that chemotherapy induces an immunogenic effect mediated by cytotoxic cells. Finally, the different deconvolution methods were benchmarked along with ConsensusTME in a pan-cancer setting by comparing deconvolution scores to DNA-based purity scores, leukocyte methylation data, and tumour infiltrating lymphocyte counts from image analysis. In so far as it has been benchmarked, unlike the other methods, ConsensusTME performs consistently among the top three methods across cancer-related benchmarks. Additionally, ConsensusTME provides a dynamic and evolvable framework that can integrate newer de- convolution tools and benchmark their performance against itself, thus generating an ever updated version. Overall, this thesis presents a systematic characterisation of the tumour microenvironment of high grade serous ovarian cancer in treatment-naive and chemotherapy treated samples, and puts forward the development of an integrative computational method for the systematic analysis of the tumour microenvironment of different tumour types using bulk RNA data.

A better understanding of tumour heterogeneity is central for accurate diagnosis, targeted therapy and personalised treatment of glioblastoma patients. This thesis aims to investigate whether pre-operative multi-parametric magnetic resonance imaging (MRI) can provide a useful tool for evaluating inter-tumoural and intra-tumoural heterogeneity of glioblastoma. For this purpose, we explored: 1) the utilities of habitat imaging in combining multi-parametric MRI for identifying invasive sub-regions (I & II); 2) the significance of integrating multi-parametric MRI, and extracting modality inter-dependence for patient stratification (III & IV); 3) the value of advanced physiological MRI and radiomics approach in predicting epigenetic phenotypes (V). The following observations were made: I. Using a joint histogram analysis method, habitats with different diffusivity patterns were identified. A non-enhancing sub-region with decreased isotropic diffusion and increased anisotropic diffusion was associated with progression-free survival (PFS, hazard ratio [HR] = 1.08, P < 0.001) and overall survival (OS, HR = 1.36, P < 0.001) in multivariate models. II. Using a thresholding method, two low perfusion compartments were identified, which displayed hypoxic and pro-inflammatory microenvironment. Higher lactate in the low perfusion compartment with restricted diffusion was associated with a worse survival (PFS: HR = 2.995, P = 0.047; OS: HR = 4.974, P = 0.005). III. Using an unsupervised multi-view feature selection and late integration method, two patient subgroups were identified, which demonstrated distinct OS (P = 0.007) and PFS (P < 0.001). Features selected by this approach showed significantly incremental prognostic value for 12-month OS (P = 0.049) and PFS (P = 0.022) than clinical factors. IV. Using a method of unsupervised clustering via copula transform and discrete feature extraction, three patient subgroups were identified. The subtype demonstrating high inter-dependency of diffusion and perfusion displayed higher lactate than the other two subtypes (P = 0.016 and P = 0.044, respectively). Both subtypes of low and high inter-dependency showed worse PFS compared to the intermediate subtype (P = 0.046 and P = 0.009, respectively). V. Using a radiomics approach, advanced physiological images showed better performance than structural images for predicting O6-methylguanine-DNA methyltransferase (MGMT) methylation status. For predicting 12-month PFS, the model of radiomic features and clinical factors outperformed the model of MGMT methylation and clinical factors (P = 0.010). In summary, pre-operative multi-parametric MRI shows potential for the non-invasive evaluation of glioblastoma heterogeneity, which could provide crucial information for patient care.

Les gliomes sont les principales tumeurs primitives du cerveau affectant environ 4000 nouveaux patients par an en France. La moitié des gliomes est détectée au stade avancé de glioblastome (grade IV) tandis que 15% des tumeurs sont diagnostiquées au stade II de gliomes diffus dit de bas grade. Ces tumeurs affectent des patients jeunes et présentent des mutations caractéristiques, notamment une mutation pour l’enzyme IDH1 communément retrouvée dans les glioblastomes secondaires. Ces tumeurs de bas grade sont traitées par une chirurgie, idéalement en condition éveillée mais du fait de leur nature diffuse, la partie résiduelle progressera inexorablement vers un stade III ou IV avec une survie globale entre 5 ans et 15 ans après diagnostique. La progression tumorale est hautement variable et non prédictible d’un patient à l’autre. Des foyers de progression tumorale chez 20% des patients atteints de gliome diffus de bas grade ont été identifiés. Ces foyers montrent une densité cellulaire plus élevée ainsi qu’un Ki67 augmenté. Mon travail de thèse aura consisté à étudier les modifications cellulaires et moléculaires associées à ces foyers de progression tumorale. À partir du profil ARN des foyers et des territoires adjacents, j’ai pu mettre en évidence par des techniques haut-débit la baisse d’expression significative de gènes dans les foyers notamment de AGXT2L1/ETNPPL, carboxypeptidase E, EDNRB, SFRP2. J’ai émis l’hypothèse que SFRP2 et ETNPLL pourraient s’opposer à la prolifération cellulaire et que leur diminution dans les foyers ouvrirait la voie à la transformation tumorale. Une corrélation inverse entre la quantité d’ETNPPL enzyme et la survie de patients atteints d’hépatocarcinomes a été publiée. En limitant la quantité de précurseurs de phospholipides dans la cellule, ETNPPL pourrait agir comme un frein en s’opposant à la prolifération et de fait, sa diminution dans les foyers de transformation des gliomes pourrait lever cette inhibition. Mes travaux auront été innovants tant dans leur approche comparative des différents compartiments tumoraux pour chaque patient étudié et auront révélés ETNPPL comme corrélé à la gliomagenèse et potentielle cible thérapeutique. / Gliomas are the main primary brain tumours affecting around 4000 new patients in France each year. Half of gliomas are detected in the advanced stage of glioblastoma (grade IV) while 15% of tumours are diagnosed in stage II (diffuse low-grade gliomas-DLGG). These tumors affect young patients and bear characteristic mutations, including a mutation for the enzyme IDH1 commonly found in secondary glioblastomas. These low-grade tumours are treated by surgery, ideally in awake condition but due to their diffuse nature, the residual part will progress inexorably to stage III or IV with overall survival between 5 and 15 years after diagnosis. Tumor progression is highly variable and unpredictable from one patient to another. Foci of tumor progression have been identified in 20% of patients with DLGG. These foci show a higher cell density and an increased Ki67. My thesis work consisted in studying the cellular and molecular changes associated with tumor progression. From the RNA profile of the foci and adjacent territories, I was able to highlight through high-throughput techniques significant decrease in gene expression in the foci, particularly of AGXT2L1/ETNPPL, carboxypeptidase E, EDNRB, SFRP2. I hypothesized that SFRP2 and ETNPLL could oppose cell proliferation and that their decrease would pave the way for tumor transformation. An inverse correlation between the amount of ETNPPL and the survival of patients with hepatocarcinoma has been published. By limiting the amount of phospholipid precursors in the cell, ETNPPL could act as a brake against proliferation and indeed, its decrease in glioma transformation foci could remove this inhibition. My PhD work will have been innovative in the comparative approach of the different tumors’ compartments for each patient studied and will have revealed ETNPPL as correlated to gliomagenesis and as potential therapeutic target.