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Serous epithelial ovarian cancer (EOC) is a potent suppressor of the immune defense. Here, we studied interactions between EOC and the immune system that lead to escape from tumor immune surveillance. We explored: 1) tumor escape from cytotoxicity by exosome-mediated modulation of the NK-cell receptors NKG2D and DNAM-1; 2) cytokine mRNA profiles in the EOC microenvironment and peripheral blood and their role in the suppression of the anti-tumor immune responses; 3) expression of long non-coding (lnc) RNAs in EOC tumors and exosomes. We found that EOC-secreted exosomes carried MICA/B and ULBP1-3, ligands of NKG2D, and could downregulate the NKG2D receptor and impair NKG2D-mediated cytotoxicity. In contrast, the DNAM-1 receptor ligands PVR and nectin-2 were seldom found in exosomes and were not associated with the exosomal membrane leaving the DNAM-1 receptor-mediated cytotoxicity intact. We compared cytokine mRNA expression in the tumor microenvironment and in immune cells of peripheral blood in EOC patients and patients with benign ovarian conditions. EOC patients were unable to mount an IFN-gamma mRNA response needed for tumor cell elimination. Instead, there was a significant up-regulation of inflammation and immune suppression i.e. responses promoting tumorigenesis and T-regulatory cell priming that suppress anti-tumor immunity. In addition, we studied lncRNAs in tissues and sera exosomes from EOC and benign ovarian conditions aiming to assess the lncRNA(s) expression profile and look for lncRNA(s) as possible marker(s) for early diagnosis. We found a deregulated lncRNAs expression in EOC tissues that correlated well with the lncRNAs expression in exosomes. Candidate lncRNAs with the highest expression and abundance were suggested for evaluation as EOC diagnostic markers in a future large cohort study. Our studies of EOC tissue and EOC exosomes highlight the immunosuppressive tumor microenvironment and the complex tumor exosome-mediated network of immunosuppressive mechanisms, and provide a mechanistic explanation of the observation that NKG2D-mediated cytotoxicity does not function in EOC patients and is partially replaced by the accessory DNAM-1 dependent cytotoxic pathway. The deregulated lncRNAs expression in EOC tissues and exosomes might serve for diagnostic purposes but could also be a potential risk of spreading tumor-derived lncRNAs in EOC exosomes to recipient cells throughout the body.

Pregnancy-related complications such as gestational hypertension, preeclampsia, fetal growth restriction, gestational diabetes mellitus, spontaneous preterm birth, and preterm premature rupture of membranes may have severe consequences for both the mother and the child. The development of reliable early screening methods for pregnancy-related complications has therefore been a long-term goal of obstetrics. New possibilities for prenatal diagnostics have opened with the discovery of circulating microRNAs in maternal plasma. MicroRNAs are short, noncoding, 21 to 23 nucleotides long, single-strand RNAs whose main function is to regulate gene expression. During pregnancy, both common and unique miRNAs are expressed by the placenta, amongst them the miRNAs of the C19MC cluster. Several C19MC miRNAs have been shown to display a different expression profile associated with certain pregnancy-related complications. This thesis identifies the plasma exosomal profiles of six C19MC miRNAs (miR-516-5p, miR-517-5p, miR-518b, miR-520a-5p, miR-520h, and miR-525-5p) in patients in their first trimester of gestation who later developed pregnancy-related complications, and compares them with profiles in patients with normal pregnancies.

Eukaryotic genomes can produce two types of transcripts: protein-coding and non-coding RNAs (ncRNAs). Cryptic ncRNA transcripts are bona fide RNA Pol II products that originate from bidirectional promoters, yet they are degraded by the RNA exosome. Such pervasive transcription is prevalent across eukaryotes, yet its regulation and function is poorly understood. We hypothesized that chromatin architecture at cryptic promoters may regulate ncRNA transcription. Nucleosomes that flank promoters are highly enriched in two histone marks: H3-K56Ac and the variant H2A.Z, which make nucleosomes highly dynamic. These histone modifications are present at a majority of promoters and their stereotypic pattern is conserved from yeast to mammals, suggesting their evolutionary importance. Although required for inducing a handful of genes, their contribution to steady-state transcription has remained elusive. In this work, we set out to understand if dynamic nucleosomes regulate cryptic transcription and how this is coordinated with the RNA exosome. Remarkably, we find that H3-K56Ac promotes RNA polymerase II occupancy at a large number of protein coding and noncoding loci, yet neither histone mark has a significant impact on steady state mRNA levels in budding yeast. Instead, broad effects of H3-K56Ac or H2A.Z on levels of both coding and ncRNAs are only revealed in the absence of the nuclear RNA exosome. We show that H2A.Z functions with H3-K56Ac in chromosome folding, facilitating formation of Chromosomal Interaction Domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA levels, perhaps in part by regulating higher order chromatin structures. Together, these chromatin factors achieve a balance of RNA exosome activity (yin; negative) and Pol II (yang; positive) to maintain transcriptional homeostasis.

Cotutelle - Mélanie Dieudé / L’ischémie-reperfusion inhérente à toute transplantation d’organe solide induit l’apoptose des cellules endothéliales. Les cellules endothéliales apoptotiques sécrètent des vésicules extracellulaires apoptotiques de type exosome (ApoExo). L’internalisation des ApoExo par les cellules endothéliales (CE) adjacentes conduit à des changements fonctionnels importants dont le dysfonctionnement endothélial. Cependant, les mécanismes d’internalisation des ApoExo par les CE sont méconnus. Des marqueurs fluorescents spécifiques aux protéines et à l’ARN ont été utilisés afin de marquer spécifiquement les ApoExo et étudier leur internalisation par microscopie confocale et cytométrie de flux. Les ApoExo ont été internalisés par les CE en fonction du temps et de la concentration. L’inhibition des voies classiques d’endocytose à l’aide d’inhibiteurs pharmacologiques et d’interférence par ARN n’a pas réduit les niveaux d’internalisation des ApoExo. Le blocage de la phosphatidylsérine des ApoExo avec l’annexine-V a réduit leur internalisation. L’analyse ultrastructurelle par microscopie électronique des CE a révélé la présence de structures lamellipodes importantes pour la macropinocytose dont l’inhibition a diminué le transfert d’ARN et de protéines dans les CE. L’analyse par RT-qPCR a révélé que l’ARNm PCSK5, le plus enrichi dans les ApoExo, est augmenté dans les CE traitées aux ApoExo. Cette augmentation est abolie avec ApoExo exempts d’ARNm PCSK5. Ces résultats démontrent que les ApoExo sont activement internalisés par macropinocytose dépendante de la phosphatidylsérine, favorisant leur internalisation en augmentant l’activité macropinocytique des CE. Les ApoExo transfèrent ainsi des ARN fonctionnels capables de moduler le protéome des CE. Ces résultats ouvrent de nouvelles portes pour la prévention de l’internalisation des ApoExo, et donc de la dysfonction endothéliale. / Ischemia-reperfusion injury inherent to solid organ transplantation induces endothelial apoptosis, releasing apoptotic exosome-like vesicles (ApoExo) which in turn induce endothelial dysfunction. We showed that ApoExo modulates gene expression, functions, and morphology of endothelial cells (EC) towards endothelial dysfunction. However, the mechanism by which EC internalize ApoExo remains unclear. Fluorescent probes specifically targeting proteins and RNA were used to track ApoExo uptake in EC by flow cytometry and confocal microscopy. Pharmacological inhibitors and gene silencing were used to probe uptake mechanisms. RNA and protein expression were quantified using Taqman RT-qPCR and immunoblot, respectively. Uptake of ApoExo by EC was observed in a time- and concentration-dependent manner. Inhibition of clathrin- and caveolae-dependent endocytosis did not decrease ApoExo internalization by EC. Blocking phosphatidylserine on ApoExo surface with annexin-V decreased ApoExo uptake. Ultrastructural analysis of serum-starved EC via electron microscopy revealed lamellipodia-like structures, hallmark of macropinocytosis, whose number increased following ApoExo exposure. Inhibition of macropinocytosis abrogated both RNA and protein transfers from ApoExo to EC. The most enriched mRNA in ApoExo, coding for PCSK5, showed enhanced levels in ApoExo-treated EC along with increased PCSK5 protein levels. This was abrogated by both macropinocytosis inhibition and depletion of PCSK5 mRNA in ApoExo. These results demonstrate that EC actively internalize ApoExo through phosphatidylserine-dependent macropinocytosis, and moreover, that ApoExo further increase macropinocytosis. These findings also show that functional RNAs can be delivered to EC through ApoExo. These results open new avenues for preventing ApoExo internalization and counteracting the development of endothelial dysfunction.

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<p>Urine-based biomarkers offer numerous advantages for clinical analysis, including non-invasive collection, a suitable sample source for longitudinal disease monitoring, a better screenshot of disease heterogeneity, higher sample volumes, faster processing times, and lower rejection rates and costs. They will be extremely useful in a clinical trial context, which can be applied alone or in combination with other methods as long as they demonstrate clear reproducibility across cohorts. While biofluids such as urine present enormous challenges with a wide dynamic range and extreme complex typically dominated by a few highly abundant proteins, we have demonstrated that the analytical issue can be efficiently addressed by focusing on extracellular vesicles (EVs), tiny packages released by all kinds of cells. These tiny packages contain different kinds of molecules from inside the cells. Here, we established a robust EV isolation and characterization platform to screen and validate Parkinson’s Disease (PD) and Renal Cell Carcinoma (RCC) biomarkers from urine. PD is a progressive neurological disorder affecting body movement because some brain cells stop producing dopamine. PD is often not diagnosed until it has advanced, making early detection crucial. We investigated urinary EVs from 138 individuals to enable early detection and found several proteins involved in PD development that could be biological indicators for early disease detection. Several biochemical techniques were applied to verify our findings. In the second project, we attempted to develop a novel diagnostic technique for early intervention of RCC. Here, we made our efforts to develop a quantitative method based on data-independent acquisition (DIA) mass spectrometry to analyze urinary EV phosphoproteomics for non-invasive RCC biomarker screening. Combined with our in-house EVtrap method for EV isolation and PolyMAC enrichment of phosphopeptides, we quantified 2,584 unique phosphosites. We observed unique upregulated phosphosites and pathways differentiating healthy control (HC), chronic kidney disease (CKD), low-grade, and high-grade clear cell RCC. These applications have a significant promise for early PD and RCC diagnosis and monitoring based on actual functional proteins with urine as the source. These studies might provide a viable path to developing urinary EV-based disease diagnosis.</p>

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