O câncer colorretal (CCR) é o terceiro tipo de câncer mais comum no mundo. Apesar dos avanços nos tratamentos convencionais, aproximadamente dois terços dos pacientes com CCR são submetidos à cirurgia potencialmente curativa. Entretanto, grande parte desses pacientes evolui mal, apresentando recidivas e/ou metástases. A busca de novos alvos moleculares para a terapia do CCR revelou a proteína celular Prion (PrPC) como um possível candidato. Trabalhos recentes sugerem participação direta ou indireta de PrPC no crescimento de tumores, na formação de metástases, na composição de complexos multiproteicos e na indução de vias de sinalização envolvidas em diversos processos biológicos, como proliferação. Além disso, PrPC foi descrito como um importante modulador do crescimento de tumor colorretal. Resultados prévios mostraram que a interação da proteína PrPC com a proteína HSP70/HSP90 Organizing Protein (HOP) induz proliferação em glioblastomas. HOP é uma proteína predominantemente citoplasmática, podendo também ser secretada associada às vesículas extracelulares. Assim, o presente estudo objetivou avaliar o papel do complexo PrPC-HOP e das vesículas extracelulares no desenvolvimento e progressão dos tumores colorretais. Os nossos resultados mostram que HOP induziu migração e invasão em linhagens de CCR de maneira dependente de PrPC, uma vez que o uso do peptídeo sem atividade que compete pelo sítio ligação de HOP a PrPC inibiu estes processos. Além disso, nossos dados apontaram que o aumento de migração e invasão das células de CCR induzida pela interação PrPC-HOP é mediada pela ativação da via ERK1/2. Os achados in vitro estimularam a avaliação do perfil de expressão de PrPC e HOP por imuno-histoquímica em tecidos de pacientes com diferentes tipos de tumores colorretais. Nossos resultados sugeriram que essas proteínas são importantes no início do desenvolvimento tumoral e na transição de adenomas para adenocarcinomas, não havendo correlação entre a presença de HOP e/ou PrPC com metástase, linfonodos acometidos, estadiamento, sobrevida ou região tumoral versus tecido normal. Em relação ao papel das vesículas extracelulares na progressão dos tumores colorretais, nossos resultados mostraram que linhagens celulares que apresentam padrões parecidos de agressividade tumoral podem ter perfis de secreção de proteínas e vesículas extracelulares bastante diferentes, induzindo, portanto, processos biológicos com intensidades distintas. O meio condicionado e as vesículas extracelulares da linhagem WiDr apresentaram maior potencial de indução de migração quando comparado com a linhagem HCT8. Além disso, a modulação negativa da proteína VPS4, uma das responsáveis pela formação dos corpos multivesiculares, mostrou-se uma abordagem interessante no estudo da secreção de vesículas por células de CCR, uma vez que o dominante negativo de VPS4 promoveu diminuição do cargo proteico e da secreção de vesículas extracelulares, redução da proliferação celular e do efeito indutor do processo de migração na linhagem WiDr. Assim, em conjunto, o presente trabalho indicou que o complexo PrPC-HOP pode ser um bom alvo terapêutico nos processos de migração e invasão em CCR. Ainda, essas proteínas se mostraram importantes nos estágios iniciais da formação dos tumores. A modulação da secreção de vesículas extracelulares pode contribuir para retardar a progressão dos tumores colorretais. / Colorectal cancer (CRC) is the third most common type of cancer in the world. Despite improvements in conventional treatments, approximately two-thirds of CRC patients undergo potentially curative surgery. However, most of these patients evolve poorly, showing recurrence and/or metastasis. Search of new molecular targets for CRC therapy revealed the cellular protein Prion (PrPC) as a putative candidate. Recent studies have shown that PrPC exhibit direct or indirect participation in tumor growth, formation of metastasis, composition of multiprotein complexes and induction of signaling pathways involved in many biological processes such as proliferation. Moreover, PrPC has been described as an important modulator of colorectal tumor growth. Previous findings showed that the interaction between PrPC and its ligand HSP70/90 heat shock organizing protein (HOP) induces gliobastoma proliferation. It is well known that HOP localizes mainly in the cytoplasm but HOP is also secreted associated with extracellular vesicles. In this way, the present study sought to evaluate the role of PrPC-HOP complex and extracellular vesicles in the development and progression of CRC. We demonstrate that HOP induces the migration and invasion of CRC cell lines in a PrPC-dependent manner because the use of HOP peptide, which is able to bind to PrPC, blocking PrPC-HOP complex formation, inhibited the migration and invasion processes. In addition, our data showed that the enhancement of migration and invasion induced by PrPC-HOP interaction is mediated by ERK1/2 pathway activation. These in vitro results lead us to evaluate the PrPC and HOP expression by immunohistochemistry in tissues from patients with different tumor types. Our data showed that these proteins could be important for the initial steps of tumor development, represented by the transition from adenoma to adenocarcinoma. No correlation was found among HOP and/or PrPC expression and metastasis, lymph node involvement, staging, survival or tumor area versus normal tissue. Regarding the role of extracellular vesicles in the progression of colorectal tumors, our results showed that cell lines exhibiting similar aggressive tumor behavior can have a different protein secretion pattern and a distinct profile of extracellular vesicles release, which could induce biological process with different intensities. The conditioned medium and the extracellular vesicles derived from WiDr cell line showed a higher potential to induce migration than HCT8 cell line. Moreover, the negative modulation of VPS4, one of the proteins responsible for multivesicular body formation, showed to be an interesting approach in the study of extracellular vesicles secretion secreted by CRC cells; the negative dominant of VPS4 promoted in the WiDr cell line a reduction in the protein cargo and secretion of the extracellular vesicles, a decrease of cell proliferation and induction of migration process. Therefore, taken together, our data highlights that PrPC-HOP complex can be considered a new therapeutic target in migration and invasion processes of CRC. Moreover, these proteins appeared to be important at onset of tumor formation. The modulation of extracellular vesicles secretion may contribute for delaying the progression of colorectal tumors.

The inflammatory arthritis Ankylosing Spondylitis (AS) is linked to the human leucocyte antigen HLA-B27. HLA-B27 is thought to drive AS because it misfolds during assembly in the endoplasmic reticulum (ER), inducing ER cell stress. Modulating HLA-B27 folding in the ER is therefore a therapeutic target pathway. The recent discovery of polymorphisms in the ER-resident peptidase ERAP1 that can impact on HLA-B27 and AS, makes ERAP1 one such target. Exosomes are small, typically 50-200 nm sized particles, formed in the endosomal recycling pathway, which can be released into the extracellular environment. Exosomes have a wide range of biological activities depending on the cell type of origin, and on the delivered cargo, which can include bio-active proteins, lipids, mRNA and miRNA. There is interest in the use of exosomes as drug delivery agents. Here, exosomes were studied as a delivery agent to modulate ERAP1, as a potential therapeutic tool for the treatment of AS. Exosomes, isolated from cell lines including CEM and Jurkat (T cell lineage), Jesthom (B cell lineage), U937 (monocyte lineage) and the epithelial HeLa cell line, were characterized by nanoparticle tracking analysis, flow cytometry and immunoblotting using markers including CD9, CD63, CD81 and TSG101. Differential expression of these markers in the immune cell lines indicated the complexity of defining exosomes. EVs were then tested using cell penetrating peptides, electroporation, lipid transfection and sonication for their ability to load FITC-siRNA or FITC-antibody as cargo. Significantly, post-loading RNase A or trypsin incubation demonstrated that many techniques do not lead to efficient cargo loading of exosomes. Sonication proved the most effective technique, with up to 30% efficiency. Loading of exosomes with ERAP1-targetted siRNA did not however lead to notable ERAP1 inhibition. The data indicates that external loading of exosomes with cargo remains a significant challenge in developing exosomes as therapeutic tools.

Extracellular vesicles (EVs) are lipid bilayer encapsulated nanoparticles which have emerged as an excellent source of biomarkers for multiple diseases, including cancer. However, they are highly heterogeneous in their molecular compositions which remains a major challenge hindering the utilization of their biomarker potential. A single-EV analysis is essential to both discovery and detect EVs that carry disease-specific signature. In this work, we designed plasmonic nanohole array for capturing single EVs and perform fluorescence detection of their membrane proteins by exploiting plasmonic amplification of the fluorescence signal. The design of the array was optimized using COMSOL Multiphysics-based simulation. Nanohole arrays with three different periodicities were fabricated on aluminum thin film on glass substrate. The substrates were then functionalized with three different methods for investigation of antibody-free capturing techniques, which are electrostatic interaction, hydrophobic interaction, and size-selective capturing. After surface functionalization with each of the techniques, genetically engineered EVs expressing mNeonGreen (mNG) were incubated and their capture efficiency were compared. The presence of single-EVs within plasmonic nanoholes was verified through both fluorescence analysis and atomic force microscopy (AFM). Fluorescence intensities of mNG-EVs recorded with the plasmonic chip with different periodicities showed intensity variations in agreement with the simulation results. Furthermore, the EVs were immunostained with R-phycoerythrin (R-PE) conjugated CD-9 to demonstrate the possibility of general and multimarker fluorescence detection. In a separate experiment, DOPC liposomes were synthesized and their deformability was analyzed by using AFM. The nanohole array provides a basis for a future platform of EV analyses, promising to capture the signature arising from low expressing proteins. / Extracellulära vesiklar (EV) är lipadmembranförsedda nanopartiklar som har dykt upp som en utmärkt källa till biomarkörer för flera sjukdomar, däribland cancer. De är dock mycket heterogena i sina molekylära sammansättningar, vilket skapar en stor utmaning och hindrar utnyttjandet av deras potential som biomarkörer. EV-analys på enpartikelnivå är nödvändig både för att upptäcka och detektera vesiklar som har en sjukdomsspecifik signatur. I detta arbete designade vi en plasmonisk uppsättning av nanohål för att fånga enstaka EVs och utföra fluorescensdetektion av deras membranproteiner genom att utnyttja plasmonisk amplifiering av fluorescenssignaler. Designen av uppsättningen optimerades med hjälp av COMSOL Multiphysics-baserad simulering. Nanohålsuppsättningar med tre olika periodiciteter tillverkades på tunn aluminiumfilm på glassubstrat. Substraten funktionaliserades sedan enligt tre olika metoder för undersökning av antikroppsfria bindningsmetoder. De tre metoderna är elektrostatisk interaktion, hydrofob interaktion och storleksselektiv bindning. Efter ytfunktionalisering med var och en av teknikerna inkuberades vesiklar genetiskt modifierade att uttrycka mNeonGreen (mNG) och deras bindningseffektivitet jämfördes. Närvaron av individuella EVs i plasmoniska nanohål bekräftades genom både fluorescensmikroskopi och atomkraftsmikroskopi (AFM). Fluorescensintensiteter för mNG-EVs registrerades med plasmonchipet med olika periodiciteter och visade intensitetsvariationer i överensstämmelse med simuleringsresultaten. Dessutom immunfärgades vesiklarna med R-fykoerytrin (R-PE) konjugerad CD-9 för att påvisa möjligheten till allmän och multimarkör fluorescensdetektion. I ett separat experiment syntetiserades DOPC-liposomer och deras deformerbarhet analyserades med AFM. Nanohåluppsättningen lägger grund för en framtida plattform för EV-analys, som lovar att fånga signaturen som uppstår från låguttryckande proteiner.

In-depth characterization has introduced new molecular subtypes of gastric cancer (GC). To identify these, new approaches and techniques are required. Liquid biopsies are trendsetting and provide an easy and feasible method to identify and to monitor GC patients. In a prospective cohort of 87 GC patients, extracellular vesicles (EVs) were isolated from 250 µL of plasma. The total RNA was isolated with TRIZOL. The total RNA amount and the relative mRNA levels of CD44, PTEN, and FASN were measured by qRT-PCR. The isolation of EVs and their contained mRNA was possible in all 87 samples investigated. The relative mRNA levels of PTEN were higher in patients already treated by chemotherapy than in chemo-naïve patients. In patients who had undergone neoadjuvant chemotherapy followed by gastrectomy, a decrease in the total RNA amount was observed after neoadjuvant chemotherapy and gastrectomy, while FASN and CD44 mRNA levels decreased only after gastrectomy. The amount of RNA and the relative mRNA levels of FASN and CD44 in EVs were affected more significantly by chemotherapy and gastrectomy than by chemotherapy alone. Therefore, they are a potential biomarker for monitoring treatment response. Future analyses are needed to identify GC-specific key RNAs in EVs, which could be used for the diagnosis of gastric cancer patients in order to determine their molecular subtype and to accompany the therapeutic response.

Venous thromboembolism (VTE), defined as deep vein thrombosis and/or pulmonary embolism is the second leading cause of mortality in cancer patients, second only to cancer itself. A number of reports suggest that circulating extracellular vesicles (EVs) may be increased in cancer patients with VTE. The aim of this study was to examine circulating EVs in high-risk ambulatory cancer patients, determine if levels are associated with hematological outcomes (VTE, major bleeding event), and to assess the impact of prophylactic antithrombotic therapy (Apixaban). We hypothesized that elevated levels of circulating large EVs will be predictive of cancer associated VTE and/or bleeding events and that treatment with Apixaban will reduce EV levels and incidence of cancer VTE. Plasma samples from patients at baseline, and 90-days follow-up from the Apixaban for the Prevention of Venous Thromboembolism in High-Risk Ambulatory Cancer patients (AVERT) trial were investigated. Total EVs were quantified by their pro-coagulant activity using the Zymuphen MP-Activity kit. Platelet, endothelial and tissue-factor EV levels were quantified by flow cytometry. We observed that circulating EVs exhibited significant associations with sex, age, and cancer type, however we did not observe any relationships with clinical outcomes. Thus, it appears that circulating EVs may not have a role in risk stratification for VTE in in high-risk ambulatory cancer patients.

Thesis with manuscript / La communication intercellulaire joue un rôle important dans tous les organismes, car elle permet l'échange de molécules bioactives entre les cellules. La plupart des cellules peuvent sécréter des vésicules extracellulaires (VE) délimitées par une membrane, qui peuvent servir de médiateur pour le transfert sélectif de matériel génétique, en particulier de molécules d'ARN, vers des cellules réceptrices et modifier leur phénotype. Pour faciliter le ciblage de l'ARN vers les VE, les protéines de liaison de l'ARN (RBP) interagissent avec les ARN, formant des complexes ribonucléoprotéiques (RNP) et guidant leur localisation vers les sites de production des VE. Alors que la facilitation du transport de l'ARN par les RBP est bien étudiée dans les cellules, leur mécanisme dans les VE reste mal compris. Pour mieux comprendre le chargement sélectif des ARN dans les VE, nous avons effectué un profilage RBP complet du sécrétome libéré par les cellules épithéliales mammaires humaines (HMLE), en comparaison avec le matériel des cellules entières. Nous avons d'abord utilisé la réticulation UV pour lier de manière covalente les RBP et leurs ARN associés, puis nous avons isolé le sécrétome par ultracentrifugation et purifié les RBP par extraction d'ARN lié à des protéines (XRNAX) et par spectrométrie de masse (MS). Grâce à une analyse comparative des RBP dans les environnements cellulaire et extracellulaire, nous avons identifié des collections de protéines associées à l'ARN qui étaient communes aux deux compartiments (n=189), ou qui présentaient une association plus spécifique avec l'ARN dans les échantillons cellulaires (n= 866) ou EV (n=502). Nous avons constaté que les RBP du compartiment extracellulaire (ExRBP) avaient des signatures fonctionnelles distinctes (par exemple, le métabolisme cellulaire, la structure et la modification des cellules, le repliement des protéines) par rapport aux facteurs enrichis en cellules (par exemple, le processus métabolique de l'ARN non codant). Notamment, des RBP EV bien connus, tels que ALIX, ANXA1, hnRNPR, hnRNPQ (SYNCRIP), YBX1, ainsi que des marqueurs EV de tétraspanine (CD9, CD81, TSG101), étaient enrichis dans l'ExRBP, ce qui indique le succès de XRNAX dans la purification des RBP EV. En comparant notre collection d'ExRBP aux signatures MS des VE plus pures dérivées des cellules HMLE, nous avons également pu délimiter les ExRBP qui vi sont susceptibles d'être enrichies en VE (PureEVRBP) par rapport à celles trouvées dans le sécrétome non VE (SecRBP). Il est frappant de constater que le PureEVRBP étaient enrichies en protéines de jonction cellulaire, tandis que le secRBP étaient enrichies en facteurs spliceosomaux, ce qui implique un chargement sélectif des RBP dans les VE ou leur sécrétion dans l'espace extracellulaire. Cette recherche fournit des informations précieuses sur la composition des RBP dans les EV, servant d'ensembles de données protéomiques clés pour élucider davantage les mécanismes modulant le recrutement sélectif des ARN dans les EV et améliorant notre connaissance des rôles des RBP dans la biologie des VE. / Intercellular communication plays an important role in all organisms, as it enables the exchange of bioactive molecules between cells. Most cells can secrete membrane-delimited extracellular vesicles (EVs), which can mediate the selective transfer of genetic material, in particular RNA molecules, to recipient cells and modify their phenotypes. To facilitate the targeting of RNA to EVs, RNA binding proteins (RBPs) are thought to interact with RNAs, forming ribonucleoprotein complexes (RNPs) and guiding their localization to sites of EV production. While the facilitation of RNA transportation by RBPs is well-studied in cells, their mechanism in EVs remain poorly understood. To gain insights into the selective loading of RNAs into EVs, we conducted comprehensive RBP profiling on the secretome released by Human Mammary Epithelial (HMLE) cells, in comparison to whole cell material. We first employed UV cross-linking to covalently link RBPs and their associated RNAs, followed by secretome isolation through ultracentrifugation and purification of RBPs using Protein-Xlinked RNA Extraction (XRNAX) and mass spectrometry (MS). Through a comparative analysis of RBPs in cellular and extracellular environment, we identified collections of RNA-associated proteins that were common to both compartments (n=189), or which exhibited more specific RNA association in cellular (n= 866) or EV (n=502) specimens. We found that extracellular compartment RBPs (ExRBPs) had distinctive functional signatures (e.g. cellular metabolism, cell structure and modification, protein folding) compared to cellular-enriched factors (e.g. non-coding RNA metabolic process). Notably, well-known EV RBPs, such as ALIX, ANXA1, hnRNPR, hnRNPQ (SYNCRIP), YBX1, as well as tetraspanin EV markers (CD9, CD81, TSG101), were enriched in ExRBP, indicating the success of XRNAX in EV RBP purification. By comparing our ExRBP collection to the MS signatures of more pure HMLE cell derived EVs, we were also able to delineate ExRBPs that are likely to be EV-enriched enriched versus those found in the non-EV secretome. Strikingly, pure EV-RBPs were enriched for cell-junction proteins, while general secretome RBPs were enriched for spliceosomal factors, implying selective loading of RBPs into EVs or their secretion into the extracellular space. This research provides valuable insights into the composition of RBPs in EVs, serving as key proteomic datasets to further elucidate iv the mechanisms modulating the selective recruitment of RNAs into EVs and enhancing our knowledge of the roles of RBPs in EV biology.

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