NCube/papyrus huggingface dataset:
Identification de dérèglements épigénétiques embryonnaires associés à une exposition prénatale à l’alcool pendant la période préimplantatoire

Prenatal alcohol exposure (PAE) is known to altered epigenetic profiles in cells during brain development and be part of the molecular basis underpinning Fetal Alcohol Spectrum Disorders (FASD) etiology. However, the consequences of a PAE during very early embryonic life on the future epigenetic landscape of embryonic and extraembryonic tissues remain unknown. Our research hypothesis is that a PAE during preimplantation will initiate DNA methylation dysregulation that will later be observable in the developing conceptus. We believe that these original epigenetic alterations will be perpetuated and amplified in the developing brain as well as in the placental tissue. To test this, we instigated FASD in mouse 8-cell embryos by injecting ethanol at 2.5 days of pregnancy (E2.5). We collected FASD (ethanol) and control (saline) E10.5 and E18.5 embryos and placentas. Dissection scoring showed an increase in morphological abnormalities in EtOH embryos of both stages. We then established genome-wide quantitative DNA methylation profiles of forebrains and placentas of E10.5 embryos by Reduced Representation Bisulfite Sequencing. Bioinformatic analyses of FASD samples (n=12) vs controls samples (n=8) revealed 686 and 2942 differentially methylated tiles (DMTs) in forebrain and placenta samples respectively. Unexpectedly, we highlighted sex-specific DNA methylation perturbations and gene expression pattern in response to ethanol exposure. Interestingly, we also uncovered 21 specific regions abnormally methylated in both FASD forebrain and placenta samples. Our study establishes for the first time that early embryonic PAE can cause epigenetic dysregulations that leads to permanent alteration in the future epigenetic program of brain and placenta cells and that some of these dysregulations are sex-specific. Altogether, our results allow us to have a better understanding of how epigenetic perturbations can alter the normal function of the brain and lead to neurodevelopmental disorders present in children with FASD.

Keyphrases: Placenta, Epigenetic, DNA methylation, Fetal Alcohol Spectrum Disorder, Prenatal alcohol exposure, Neurodevelopmental disorders, Embryonic development, Brain, Epigenetic reprogramming, Maternal environment
« S’il faut rapatrier tout ce qui est sacré, c’est la terre qui va venir à nous ». Le processus de rapatriement des objets culturels et sacrés des Ilnuatsh de Mashteuiatsh, au Québec

The repatriation of cultural and sacred indigenous objects has animated the international scene for more than thirty years. However, few studies focus on the sociocultural and identity issues underlying the diversity of indigenous requests. This thesis explores the particularities of a repatriation process of cultural and sacred objects: the one led by the Mashteuiatsh ilnu community in Quebec with the National Museum of the American Indian (NMAI), Washington DC. Through what mechanisms and according to what stakes does the repatriation process give the Ilnuatsh the power to define, update and regain control over the cultural contents that constitute their cultural identity? How can this process engage a reflexive process of defining and asserting their cultural heritage and their way of being in the world ? By crossing the ethno-historical study with the ethnographic approach, our methodology is rooted in an ethically involved approach within a collaborative research project. Following the theoretical and methodological avenues developed by the biographical and agentive approaches of objects, the study traces the life course of three types of ilnu objects preserved in NMAI: two nimapan (portage straps), a mushianiakup (moose-skin coat) and two teuehikan (drums). We first analyze how the knowledge related to these objects was built up in a collaborative process shared across several generations of Ilnuatsh. Then, we analyze how the Ilnuatsh appropriate the repatriation framework imposed by the NMAI: how do they use the objects and related knowledge to fuel forms of justification that reinforce the recognition of their cultural distinctions? To answer this question, we focus on issues related to identity affiliation and the conceptualization of "sacred" objects. The ilnu notion of "sacred object" developed in this thesis contrasts with the conceptual categories imposed by the NMAI. It highlights in particular the complexity of the relational network in which objects are invested ; a network which is evolving today in contexts of identity and cultural affirmation and legitimation.

Keyphrases: Pekuakamiulnuatsh, Mashteuiatsh, Recherche collaborative, Frank G. Speck, Repatriation, Cultural objects, Sacred objects, Identity affirmation, Museology, Collaborative research, National Museum of the American Indian
L’impact des technologies d’anonymat sur les conflits impliquant des vendeurs dans les marchés de drogues

This research aims at understanding the impact of anonymity technologies on conflicts regarding drug vendors. Data comes from an online survey hosted on Tor answered by dealers, ages 18 and older, that sold drugs on cryptomarkets in the past twelve months. Results are mixed. It seems like more serious victimisations, like armed threats and physical attacks, happen more frequently in traditional offline drug dealing. The same can be said about deceptive transactions, where the quality or the quantity of the drug is less than advertised. Yet, thefts and theft attempts of over 500 $ and unarmed threats are more frequent when the transactions happen online. Additionally, drug vendors who sell amphetamine suffer significantly more conflicts than those who do not.

Keyphrases: Violence, Dark Net, Cryptomarkets, Drug trafficking, Conflict
Analyses intracellulaires des interactions et de la signalisation de la polycystine-1

Autosomal dominant polycystic kidney disease (ADPKD) affects 1/500 person, causes renal cysts and leads to kidney failure. It depends on a dosage effect mechanism of one of the PKD1 or PKD2 genes encoding polysystin-1 and polycystin-2 (Pc1, Pc2), respectively. The polycystins form a complex via their coiled-coil domains. A murine Pkd1-BAC was modified by homologous recombination to produce a full-length transcript (Pkd1TAG-BAC). Overexpression of Pkd1 in Pkd1TAG mice induces polycystic kidney disease (PKD). To define the intracellular role of the coiled-coil motif of Pc1, the motif was deleted from Pkd1 by recombination and used to generate four Pkd1Δcoiled-coil mouse lines (1-10 copies). These mice do not develop PKD. The coiled-coil motif is therefore required to induce the disease. In mice, the knock-out of Pkd1 causes PKD and perinatal mortality. We therefore produced Pkd1-/-; Pkd1TAG and Pkd1-/-; Pkd1Δcoiled-coil mice. These are protected from perinatal mortality and PKD, but 1-3 copy lines act as functional hypomorphs. Pkd1Δcoiled-coil kidney cells show that Pc1 is sufficiently efficient in maturation and intracellular trafficking, that the interaction is conserved between Pc1-Pc2 and that Pc2 expression is unchanged except in hypomorphs where Pc2 is overexpressed. The coiled-coil motif of Pc1 and its interactions appear to induce polycystic kidney disease and play a role in renal homeostasis.

Keyphrases: PKD, coiled-coil, interactions, maturation, polycystins, mouse, trafficking
Étude des conséquences fonctionnelles de la mutation SGO1 K23E sur la voie de signalisation TGF-β

We recently identified a novel generalized dysrhythmia syndrome in the French-Canadian population that we termed CAID syndrome (Chronic Atrial and Intestinal Dysrhythmia), caused by a recessive homozygous mutation in the gene Shugoshin-like 1 (SGO1). The mutation changes a lysine by a glutamic acid at the position 23. All patients have sick sinus syndrome as well as chronic intestinal pseudo-obstruction, making it the first generalized pace making syndrome affecting both the cardiac and the intestinal pacemaker.  We previously have shown that the SGO1 K23E mutation affect the TGF-ß signaling pathway, which is involved in many crucial biological process, although the role of SGO1 in this pathway has not been well characterized. A study identified the BUB1 protein involved in the centromeric localization of SGO1, as regulator of this pathway (2015). This suggests a possible implication of SGO1 in this process. The objective of this Master project is to characterize this new role of SGO1 during the sinus node development, and the impact of the K23E mutation. The phosphorylation state of some proteins involved in this TGF-β pathway has been quantified in skin fibroblasts of both patients and controls, by using the ALPHA technology (Amplified Luminescence Proximity Homogenous Assay), and the results reveal that the K23E mutation induces an increase of the canonical TGF-β pathway and also, an inhibition of the non-canonical pathway.

Keyphrases: Syndrome CAID, CAID syndrome, Sick Sinus Syndrome, Chronic and Intestinal Pseudo-Obstruction, SGO1 protein, Cohesinopathy, TGF-β signaling, Cellules hiPS, hiPS cells, Cardiac differentiation, Protein quantification
Déterminants biochimiques, génétiques et épigénétiques de l’encéphalomyélite myalgique

Myalgic encephalomyelitis (ME) is a chronic and complex disease characterized by recurrent and persistent fatigue that lasts for 6 months or more and is associated with pain and an abundance of other symptoms (1,2). Among the biomarkers tested, we measured plasma homocysteine (Hcy) in our ME cohort (N = 112) as well as in an age- and sex-matched group of healthy controls (N = 58). Patients and control subjects were stratified according to their Hcy plasma levels. Hyperhomocysteinemia (>15 µmol/L) was observed at a higher frequency in the EM patients (22.3%) than in the control group (15.5%), while the frequency of hypohomcysteinemia (<5 µmol/L) was 32.1% in EM patients and 50% in controls.  The aim of this study was to better understand the contribution of Hcy in the exacerbation of ME symptoms, as well as to elucidate the molecular and genetic mechanisms associated with moderate hyperhomocysteinemia and hypohomocysteinemia in patients with myalgic encephalomyelitis. Standardized questionnaires (DSQ, MFI-20 and SF-36) revealed clinical differences between the subgroups. In particular, hypohomocysteinemia was associated with an exacerbation of neurological symptoms in some ME patients, while hyperhomocysteinemic ME patients had higher scores for post-exertional malaise (P <0.05). In this context, we investigated the contribution of nutritional cofactors (vitamins B6, B12, C and folate) and genetic factors in gene variants associated with the Hcy metabolic pathway or with vitamin receptors and transporters. The urinary and plasmatic levels of vitamins B6, B12, C and folate were measured by ELISA. Hyperhomocysteinemic ME patients did not show any nutritional deficiencies, unlike the subpopulation of hyperhomocysteinemic control subjects. At the genomic level, we also genotyped 110 SNPs known to regulate plasmatic levels of Hcy. In a first genotypic analysis between ME patients and controls, the SNP rs7703033 (MTRR) had a strong association with the disease. In addition, this work demonstrated an association between SNP rs1801198 (TCN2) and hypohomocysteinemia in ME patients. Moreover, mean plasmatic levels of vitamin B12 were higher in these ME patients. A strong association was found between certain SNPs such as rs2124459 (CBS), rs17367504 (MTHFR), rs4257763 (SLC23A1) and rs1195646 (SLC23A2) and hyperhomocysteinemia in ME patients.  These results demonstrate that circulating levels of Hcy exacerbate the symptoms of the disease in people with ME in the Quebec population in Hcy because of genetic predispositions that differentiate subjects with specific subgroups.

Keyphrases: Vitamines B6 - B12 - C – folate, microARN, Myalgic encephalomyelitis (ME), Hyperhomocysteinemia, Vitamins B6 - B12 - C – folate, Single nucleotide polymorphism (SNP), Genotyping, microRNA
Impact de différentes modalités de recrutement de la β-arrestine au récepteur de chimiokine CXCR4

Chemokines are small proteins involved in cell migration. The chemokine CXCL12  (SDF-1) signals via the receptor CXCR4. CXCR4 is overexpressed in more than 20 types  of cancer, and associated with metastasis and increased cancer cell growth and survival.  The diversity and complexity of CXCR4 signaling are subject to research, but CXCR4  signals through two major pathways: Gαi and β-arrestin 2. Regulatory mechanisms for β-  arrestin recruitment remain to be defined, but the recent interpretive framework describes  a two-stage recruitment mechanism allowing for two levels of interaction. The first step  would allow binding of the C-terminal end of the receptor to β-arrestin, forming a partial  interaction, while the second would allow subsequent binding of β-arrestin to the core of  the receptor, forming a complete interaction.  This project studies these different recruitment modalities using the constitutively  active mutants of CXCR4; N119S and R134A, using bioluminescence resonance energy  transfer (BRET) systems. We confirmed that CXCR4 N119S is a constitutively active  mutant (CAM) on both Gαi and the arrestin pathway. On the other hand, R134A is a  constitutively inactive mutant (CIM), thus lacking signaling by the G protein, but  spontaneously recruits β-arrestin.  We suggest that the differences in recruitment of β-arrestin observed in BRET  between these two mutants represent these different recruitment modalities. Thus, the  mutant N119S represents the complete interaction while the mutant R134A represents the  partial interaction. Similarly, we observe differences between these mutants in activation  of ERK by Immunoblot. Finally, the use of PTX, inhibiting the activation of Gαi,  demonstrates that the mutant R134A recruits β-arrestin through a different modality. We  suggest that this mutant allows the formation of a megaplex between β-arrestin and the  heterotrimeric G-protein.

Keyphrases: CXCR4, β-arrestin, GRK, BRET, WHIM
Auto-renouvellement et reprogrammation oncogénique dans les leucémies aiguës

Although the leukemogenic process can differ between acute leukemia subtypes, several oncogenes are known to confer aberrant self-renewal properties to hematopoietic progenitors. As a result, these self-renewing cells persist in vivo and can acquire additional mutations, thus leading to leukemia development or relapse after treatment. We have identified two novel mechanisms by which the SCL and LMO1 oncogenes in T-cell acute lymphoblastic leukemia and the MLL-AF6 oncogene in acute myeloid leukemia promote self-renewal and oncogenic reprogramming. In the T-ALL model, we previously showed that transcriptional activation by the SCL and LMO1 oncogenes is required for oncogenic reprogramming and T-ALL development. We now identify a novel mechanism where transcriptional down-regulation of ribosomal protein gene expression in pre-leukemic thymocytes results in a concomitant decrease in cell size and in protein synthesis. This is associated with decreased cell proliferation and sustained self-renewal, which altogether contributes to SCL and LMO1 oncogenic reprogramming and the emergence of pre-LSCs. Furthermore, the acquisition of NOTCH1 mutations leading to overt T-ALL is associated with an increase in cell size, protein synthesis and ribosomal protein gene expression, suggesting that a switch from low to high protein synthesis rates may be important for leukemia progression. In the AML model, we found that MLL-AF6 translocations result in the loss of a conserved N-terminal alpha-helix in the first RAS-association domain of AF6. This induces protein fusion dimerization and confers aberrant self-renewal activity to myeloid progenitors. Strikingly, reinsertion of the alpha-helix completely hinders dimerization and thus, abrogates self-renewal and leukemogenesis. Taken together, our results demonstrate that self-renewal is a critical determinant of oncogenic reprogramming and offer new therapeutic strategies in acute leukemia.

Keyphrases: MLL-AF6, Self-renewal, Oncogenic reprogramming, Acute leukemia, SCL and LMO1, Pre-leukemic stem cells, Leukemia-propagating cells, Protein synthesis, Ribosome biogenesis, Dimerization
Aiming to identify protein co-factors contributing to eIF4E’s oncogenic potential

The eukaryotic Initiation Factor 4E (eIF4E) regulates cell growth and proliferation via two independent functions. In the cytoplasm, eIF4E promotes translation of mRNAs with complex 5’UTRs. In the nucleus, eIF4E specifically promotes the export of mRNAs of oncogenes such as c-myc, via an eIF4E-dependent, CRM-1 mediated export pathway, distinct from the bulk mRNA export pathway. In this pathway, eIF4E interacts with both the m7G-cap and with a structurally conserved, 50 nucleotides long, 3’UTR 4E-Sensitive Element (4E-SE). Elevated eIF4E levels are found in ~ 30% of cancers, including Acute Myeloid Leukemia (AML). Interestingly, the eIF4E-S53A mutant, active in translation, does not function in export and is unable to transform cells, suggesting that eIF4E’s role in mRNA export is necessary to transform cells. These findings led us to the following Hypothesis: Protein co-factors binding at the Ser-53 site are crucial for eIF4E’s role in export and for the oncogenic transformation potential of eIF4E. The objectives were to achieve a better understanding of how eIF4E-mRNPs assembly and export works, examining the protein composition of nuclear eIF4E-mRNPs, and using eIF4ES53A mutant to retain protein factors that require Ser53 as candidates for being strong drivers of eIF4E oncogenic potential. Studies into eIF4E and S53A eIF4E cell lines were undertaken. U2OS cell lines expressing wild type eIF4E and the S53A mutant were generated. IP studies with FLAG antibodies on the whole-cell and nuclear lysates of U2OS cell lines were carried. This project laid the groundwork for future insights into how biochemical activities of 4ESEbearing mRNAs influence their export.

Keyphrases: eIF4E, eIF4E-mRNP, MutantS53A, Nuclear export, Oncogenic potential, eIF4E-mRNPs
Studying cross-talk between different transcriptional pathways controlling azole resistance in Candida albicans

Tac1p and Mrr1p are both important transcriptional regulators of azole resistance in the yeast Candida albicans. Gain-of-function mutations in these factors are responsible for the constitutive upregulation of azole resistance genes in several C. albicans clinical isolates. Both factors can also be transiently activated by specific chemical compounds. Based on the results suggesting that these two pathways may interact, we studied whether Mrr1p is involved in the Tac1p-mediated transcriptional pathway. First, we investigated whether Mrr1p functions in fluphenazine-induced transient upregulation of CDR1 and TAC1, both of which are Tac1p target genes and encode important effectors of azole resistance. The results suggest that Mrr1p plays a complicated role in this process and might suppress the transient induction of TAC1. Second, we studied the role of Mrr1p in hyperactive Tac1p-mediated constitutive upregulation of CDR1 and TAC1 as well as the resulting azole resistance in a well-characterized azole-resistant clinical isolate 5674. We found that Mrr1p contributes to the resistance of isolate 5674 to fluconazole, but that the deletion of MRR1 in isolate 5674 had no impact on the mRNA levels of CDR1 and TAC1. Moreover, we have also shown that the TAC1 transcripts in isolate 5674 have a long 5’ untranslated region and that Mrr1p is not implicated in producing this long TAC1 mRNA. Since some of the results are preliminary, further experiments will be needed to confirm these results and address remaining questions.

Keyphrases: Candida albicans, TAC1, MRR1, Azole resistance, Homologous recombination, Transcription factor, Fluphenazine, Upregulation
Le rôle de Ral dans la migration collective des cellules de bordures

Metastasis formation is the primary cause of lethality in cancer. Ral is a small GTPase which has been involved in metastatic invasion though many of its effectors. A powerful model to study collective cell migration is border cells in Drosophila melanogaster. Border cells migrate through nurse cells until they reach the oocyte.   The goal of my master project is to characterize the role of Ral in border cell migration. I hypothesize that Ral regulates the exocyst complex which allows the polarisation of migration determinants.  Using the Gal4-UAS system, RNAi of Ral, Ral GEFs and Ral GAP have been expressed in the cluster. The depletion of Ral induces a migration defect, while the depletion of Ral GEF and Ral GAP does not induce a migration defect nor increase the migration defect seen with Ral. Furthermore, we tested which migration determinant was affected by Ral depletion and we found that the polarization of receptor tyrosine kinase (RTKs) was lost after depletion of Ral.  Next, effectors of Ral were depleted in the border cell cluster. While Rlip depletion did not induce migration defects, depletion of several subunits of the exocyst complex affected migration. To determine if Ral is acting through the exocyst, mutants of Ral that cannot bind the exocyst were expressed. Surprisingly, the mutant rescues the phenotype induced by Ral depletion suggesting that the function of Ral in border cells is independent of its binding to the exocyst complex.  To conclude, I showed that Ral is implicated in border cell migration. The action of Ral in this process seems to be independent of its GTPase activity. Furthermore, I showed that Ral is implicated in the polarisation of RTKs at the front of migration.

Keyphrases: Ral, RTKs, Metastasis, Drosophila, Exocyst
Rôle de la méthylation de l’ADN dans la régulation de l’expression des gènes 15-LOX-1 et 15-LOX-2 dans le cartilage

Osteoarthritis is characterized, among other things, by the breakdown of articular cartilage and the inflammation of the synovium. These features are due to increased synthesis of pro-inflammatory and catabolic mediators. The molecular mechanisms underlying these changes are poorly known. Preliminary work indicates that the 15-LOXs genes have an anti-catabolic and anti-inflammatory role and that their expression is decreased in OA cartilage. Our hypothesis is that DNA methylation of the proximal promoters of the 15-LOX-1 and 15-LOX-2 genes inhibits their expression in OA cartilage. Our goal is to determine whether there is a correlation between their expression and the methylation of their promoters. Expression of these genes in both OA and normal cartilage was evaluated by immunohistochemistry and real-time RT-PCR. The effect of 5-AZA, a demethylating agent, on their expression was evaluated by RT-PCR. The methylation levels of their proximal promoters in degraded or intact osteoarthritic cartilage were evaluated by pyrosequencing. Our results showed a decrease in 15-LOX gene expression in OA cartilage. We also observed a significant increase in 15-LOXs gene expression upon treatment with 5-AZA-DC. In addition, we demonstrated that there were no differences in the methylation levels of CpG sites of 15-LOXs gene promoters between degraded and intact osteoarthritic cartilages. Methylation rates of CpG sites are generally low These results suggest that repression of 15-LOXs gene expression in osteoarthritic cartilage is not due to DNA methylation.

Keyphrases: Osteoarthritis, DNA methylation, Regulation of gene expression 15-LOXs