Submitted by Luciana Sebin (lusebin@ufscar.br) on 2016-09-28T18:55:34Z No. of bitstreams: 2 TesePRMM.pdf: 7211801 bytes, checksum: 788705ca3b95b2f530d64b669f066f88 (MD5) TesePRMM.pdf: 7211801 bytes, checksum: 788705ca3b95b2f530d64b669f066f88 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-10-10T18:35:31Z (GMT) No. of bitstreams: 2 TesePRMM.pdf: 7211801 bytes, checksum: 788705ca3b95b2f530d64b669f066f88 (MD5) TesePRMM.pdf: 7211801 bytes, checksum: 788705ca3b95b2f530d64b669f066f88 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-10-10T18:35:43Z (GMT) No. of bitstreams: 2 TesePRMM.pdf: 7211801 bytes, checksum: 788705ca3b95b2f530d64b669f066f88 (MD5) TesePRMM.pdf: 7211801 bytes, checksum: 788705ca3b95b2f530d64b669f066f88 (MD5) / Made available in DSpace on 2016-10-10T18:35:56Z (GMT). No. of bitstreams: 2 TesePRMM.pdf: 7211801 bytes, checksum: 788705ca3b95b2f530d64b669f066f88 (MD5) TesePRMM.pdf: 7211801 bytes, checksum: 788705ca3b95b2f530d64b669f066f88 (MD5) Previous issue date: 2016-03-11 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / ADAM10 is an-secretase that cleaves APP in the non-amyloidogenic pathway, thereby inhibiting -amyloid peptide (A ) production in Alzheimer´s disease (AD). Studies have shown decreased ADAM10 platelet levels in AD patients as well as the deregulation of microRNAs (miRNAs) related to molecules involved in the pathophysiology of this disease. The objective was to verify and compare ADAM10 gene expression and micro-RNAs (miRNAs) between AD patients and controls without cognitive impairment. It is a comparative study, based on the assumptions of quantitative research. Biological samples were collected, analyzed and stored in a biorepository. The ADAM10 gene expression in whole blood was studied in 47 AD, 32 healthy controls and 21 mild cognitive impairment (MCI) subjects by RT-qPCR techniques and analyzed by relative expression by 2- Ct. For miRNAs analyses, using MegaplexTM and MirWalk 2.0 database, were analyzed by RT-qPCR ~700 miRNAs in total blood and 21 miRNAs of them were validated in a sample of 21 AD subjects and 17 healthy controls. Statistical association tests, regression and diagnostic accuracy were performed. No significant differences in ADAM10 gene expression were observed between AD and control groups. Therefore, the decrease of ADAM10 protein in platelets of AD patients was not caused by a reduction in mRNA encoding for ADAM10. Mir-144-5p, miR-374 and miR-221 were downregulated in AD subjects, with moderate accuracy diagnosis. However, the association of selected miRNAs expression and Mini Mental State Examination (MMSE) was significantly better as a diagnostic tool compared to their expression separately. The validated miRNAs are involved in the regulation of pathways related to neurodegenerative diseases (beta-amyloid cascade, ubiquitination, transcriptional regulator, synaptic transmission, vesicle trafficking). Specifically, miR-144-5p, miR-374 and miR-221 are relevant for AD, as regulators of APP, BACE1 and ADAM10 translation. To the best of our knowledge, this is the first study to demonstrate a downregulation of these specific miRNAs in total blood of Alzheimer’s disease patients, compared to healthy cognitive controls. These findings are in agreement with AD protein outcomes and place the miRNAs evaluated as potential biomarkers that can be used to improve AD diagnosis. / ADAM10 é uma -secretase que cliva a APP através do caminho não amiloidogênico, inibindo desta forma a produção do peptídeo -amiloide (A ) na doença de Alzheimer (DA). Estudos apresentam a diminuição plaquetária da proteína ADAM10 em idosos com DA, assim como a desregulação de microRNAs (miRNAs) relacionados com moléculas envolvidas com a fisiopatologia desta doença. O objetivo geral foi verificar e comparar a expressão gênica da ADAM10 e de miRNAs entre idosos com DA e controles sem alterações cognitivas. Trata-se de um estudo de comparação, baseado nos pressupostos da pesquisa quantitativa. Amostras biológicas foram coletadas, analisadas e armazenadas em um biorrepositório. A expressão gênica da ADAM10 em sangue total foi estudada em 47 sujeitos com DA, 32 controles saudáveis e 21 sujeitos com transtorno neurocognitivo leve (TNCL), através de técnicas de RT-qPCR e analisada pela expressão relativa por 2- Ct. Para análises dos miRNAs, utilizando Megaplex e a base de dados MiRWalk 2.0, foram analisados por RTqPCR ~700 miRNAs no sangue total e 21 deles foram validados em uma amostra de 21 sujeitos com DA e 17 controles. Testes estatísticos de associação, regressão e acurácia diagnóstica foram realizados. Não foi observada diferença significante na expressão gênica da ADAM10 entre sujeitos com DA e controles. Assim, a diminuição dos níveis proteicos da ADAM10 plaquetária em pacientes com DA não foi devido a redução do mRNA codificante para ADAM10. Mir-144-5p, miR-374 e miR-221 estavam menos expressos em indivíduos com DA, com moderada acurácia diagnóstica. Entretanto, a associação da expressão dos miRNAs selecionados com o Mini Exame do Estado Mental (MEEM) foi significativamente melhor como uma ferramenta de diagnóstico em comparação com as análises individuais. Os miRNAs validados estão envolvidos na regulação de vias relacionadas a doenças neurodegenerativas (cascata beta-amiloide, ubiquitinação, reguladores de transcrição, transmissão sináptica, tráfego de vesículas). Especificamente, o miR-144-5p, miR-374 e miR- 221 são relevantes para a DA, como reguladores da tradução da APP, BACE1 e da ADAM10. Segundo nosso conhecimento, este é o primeiro estudo a demonstrar a expressão reduzida desses miRNAs no sangue total de pacientes com DA, em comparação com controles cognitivamente saudáveis. Estes resultados estão de acordo com os resultados proteicos da DA e destacam os miRNAs avaliados como potenciais biomarcadores que podem ser utilizados para o aperfeiçoamento do diagnóstico da DA.

O câncer de próstata é a segunda causa de morte entre homens no Brasil. É tipo um câncer de crescimento lento, podendo levar anos para o tumor atingir 1 cm3, porém, em alguns casos ele pode se espalhar pelo corpo, sendo o osso o principal sítio de metástase. No estágio de desenvolvimento do câncer conhecido como metástase, o principal tratamento consiste em terapia de restrição andrógena, levando as células prostáticas a pararem de proliferar, uma vez que elas crescem em resposta a presença de hormônios andrógenos, como a diidrotestosterona e testosterona. Porém, em alguns casos, as células proliferam mesmo na ausência de andrógenos e isto se deve a diversos fatores que, em geral, estão associados a mutações no receptor andrógeno e/ou alterações no metabolismo andrógeno. Quando isto acontece, os tratamentos disponíveis são menos efetivos e costumam falhar. Porém, estudos sugerem que o γ-orizanol, um fitoesterol extraído do óleo do farelo do arroz; e extratos amplamente utilizados na medicina popular, como o extrato hidroalcólico de Thuya occidentalis, poderiam atuar inibindo o desenvolvimento e progressão do câncer de próstata. Neste estudo, com o uso de abordagens bioquímicas e de biologia molecular, foi demonstrado que o tratamento com γ-orizanol diminui a viabilidade e biomassa celular em cultura, associado ao aumento da morte celular por apoptose e/ou necrose, em linhagens celulares responsivas (LNCaP) e não-responsivas a andrógenos (PC3 e DU145), além de aumentar a pERK1/2 em células LNCaP e DU145. O γ-orizanol também foi capaz de bloquear o ciclo celular em G2/M nas células PC3 e LNCaP e em G0/G1 nas células DU145. Estes efeitos foram ainda acompanhados por uma redução da expressão do gene e proteína caveolina-1- uma importante molécula envolvida no aumento da agressividade do câncer de próstata, e também, na progressão da doença para o fenótipo andrógeno resistente - nas células não-responsivas a andrógenos, e do gene PCGEM1 - gene específico da próstata regulado por andrógeno - nas células LNCaP e DU145. Ainda, γ-orizanol também mostrou capacidade de regular vários miRNAs - pequenas moléculas de RNA não codificantes de proteínas - envolvidos no controle de funções associadas ao desenvolvimento, progressão e invasão no câncer de próstata, como o miR16-1, miR19b-2, miR24b-1, miR24b-2, miR99a, miR133a-5p, miR182-5p, miR198 e miR222. O extrato hidroalcólico de Thuya occidentalis reduziu a viabilidade e biomassa celular nas linhagens responsiva (LNCaP) e não-responsivas (DU145 e PC3) a andrógenos, além de induzir parada do ciclo celular na fase G0/G1 nas células DU145 e aumentar a morte celular por apoptose e/ou necrose em todas as linhagens. Da mesma forma que o γ-orizanol, este extrato reduziu a expressão da caveolina-1 nas linhagens não-responsivas a andrógenos. Trabalhos anteriores mostram que o monoterpeno α-tujona é o principal composto ativo do extrato de Thuya occidentalis. Por cromatografia gasosa acoplada a detector de massas foi mostrada a existência de 0,0016 μg de α-tujona na dose de extrato usada neste estudo. No entanto, o tratamento com 0,0016μg de α-tujona foi efetivo somente sobre linhagem LNCaP, não tendo efeito sobre as outras linhagens estudadas, reforçando a hipótese da diferença de sensibilidade entre as linhagens responsivas e não responsivas a andrógeno e mostrando a contribuição de outros componentes do extrato nos efeitos observados neste estudo. Concluindo, estes resultados demonstram que tanto γ-orizanol como o extrato de Thuya occidentalis podem vir a ser agentes terapêuticos promissores no tratamento de câncer de próstata, não só por inibirem o crescimento celular, mas também e principalmente pela possibilidade de induzirem a recuperação da sensibilidade a andrógenos, aumentando as possibilidades de tratamento da doença. / Prostate cancer is the second cause of death among men in Brazil. It is a slowgrowing cancer and it may take years for tumor to reach 1 cm3, but in some cases it can spread throughout the body and the bone is the main site of metastasis. At this cancer stage known as metastasis, the principal treatment involves antiandrogen therapy, leading to prostate cells stop proliferating, because they grow in response to presence of androgens such as testosterone and dihydrotestosterone. However, in some cases, the cells can proliferate even in the absence of androgens and this fact occurs due to many factors and they are generally associated with mutations in the androgen receptor and/or alterations in androgen metabolism. In this stage, the treatments available are less effective and usually fail. However, studies suggest that γ-oryzanol, a phytosterol extracted of rice bran oil; and extracts widely used in folk medicine, as Thuya occidentalis hidroalcolic extract, could act inhibiting the development and progression of prostate cancer. In this study, using molecular biology and biochemical approaches we showed that γ- oryzanol treatment was able to decrease cell viability and biomass in culture, and this fact was linked to increased cell death by apoptosis and/or necrosis in androgen responsive (LNCaP) and unresponsive (DU145 and PC3) prostate cancer cell lines, besides increasing pERK1/2 in LNCaP and DU145 cells. γ- oryzanol was also able to cause cell cycle arrest at G2/M phase in LNCaP and PC3 cells and at G0/G1 phase in DU145 cells. These effects were also accompanied by a reduction in caveolin-1 gene and protein expression - an important molecule related to high aggressiveness in prostate cancer and also in the progression of the disease to androgen resistant phenotype - in androgen unresponsive cells, and also PCGEM1 gene - a prostate specific gene regulated by androgens - in LNCaP and DU145 cells. γ-oryzanol also showed ability to regulate several miRNAs - small non-coding RNA molecules - involved in the control of many functions associated with the development, progression and invasion of prostate cancer, such as miR16-1, miR19b-2, miR24b-1, miR24b-2, miR99a, miR133a-5p, miR182-5p, miR198 and miR222. Thuya occidentalis hidroalcolic extract also reduce cell viability and biomass in androgen responsive (LNCaP) and unresponsive (DU145 and PC3) cells, in addition to inducing cell cycle arrest at G0/G1 phase in DU145 cells and to increase apoptosis and/or necrosis cell death in all cell lines. The same way that γ-oryzanol, this extract reduced the caveolin-1 expression in androgen unresponsive prostate cancer cells. Prior studies showed that the monoterpene α-thujone is the main active compound in the T. occidentalis extract. By gas chromatography coupled to mass detector it was showed the existence of 0.0016 μg of α-thujone in extract dose used in this study. However, the treatment with 0.0016 μg of α-thujone was effective only on LNCaP cell line, having no effect on the other studied lines, supporting the hypothesis of difference in sensitivity between responsive and unresponsive cell lines and showing the contribution of other components in the effects caused by the extract, observed it this study. In conclusion, these results demonstrate that both γ-oryzanol as T. occidentalis extract may become promising therapeutic agents in treatment of prostate cancer, not only inhibit cell growth but also and manly by the possibility of inducing the recovery of androgen sensitivity, increasing the treatment chances of treatment this disease.

The glial cells of the brain and the peripheral nervous system retain the capacity to divide and proliferate throughout the lifespan of an individual and thereby have the propensity to give rise to the most adult neurological tumours. Among them, the tumours which arise from different kinds of glial cells are referred to as gliomas. Of the various types of gliomas, astrocytomas are the most common central nervous system neoplasms which make upto 60% of all the primary brain tumours. Being the most prevalent type, the WHO classifies them into grades ranging from I to IV based on their intensity of malignancy. Grade IV astrocytoma or Glioblastoma (GBM) is considered to be the most malignant form with a median survival of 14.6 months, in spite of all therapeutic modalities. GBM is further classified as primary and secondary GBM. Primary GBM manifests de novo without any early history of pre-malignant lesions, on the other hand secondary GBM arises progressively from lower grades over a period of 5-10 years. Like other malignancies, GBM also arises from various genetic and epigenetic variations. Epigenetic variations include all such mitotically and meiotically heritable traits that do not involve changes in DNA sequence. There are three major areas of epigenetics - DNA methylation, histone modifications and non-coding RNAs which are known to have profound effects on gene expression. A lot being known about the genetic derailments in GBM, in this study we looked into the epigenetic aspects of GBM. In our lab, we have carried out various high throughput studies, which unveiled the distorted landscape of DNA methylation and miRNA expression in GBM. This indicates that, in addition to the genetic mechanisms of gene alterations like mutations, copy number aberrations, protein coding genes are also affected by changes in methylation as well as by miRNA misregulation. The study has been divided into two parts. Part one of the study deals with the identification of chromobox homolog 7 (Cbx7), as a hypermethylated and downregulated gene in GBM. More importantly, Cbx7 is a member of the polycomb repressive complex and brings about its function through chromatin modifications. Here we have investigated the role of Cbx7 in gliomagenesis, and why it has to be silenced by methylation for tumorigenesis to ensue. In part two, we elucidated two unique ways of miRNA regulation in GBM. In the first section, we identified miR-326 as a PI3 kinase regulated miRNA and demonstrated its tumour suppressive role in GBM. In the other section, we analysed the copy number aberration data from TCGA and identified miR- 4484 as a miRNA subjected to deletion in GBM. We further went ahead to demonstrate its growth suppressive role in GBM. Part 1: Epigenetic regulation of the chromatin modifier Cbx7; chromobox homolog 7 DNA methylation is involved in the normal cellular control of expression and thereby plays a crucial role in maintaining the homeostasis of the cell. The phenomenon of DNA methylation keeps the various loci of the genome such as the germline specific genes and the repetitive transposable elements silenced, whereas the tumour suppressors and other growth modulator genes are spared from the methylation induced gene repression. One of the important steps that promote tumorigenesis is aberrant hypermethylation, which leads to the silencing of tumour-suppressor genes. Another important epigenetic phenomenon that affects the transcriptibility of the genome is histone modifications, which control the accessibility of the chromatin to the transcriptional machinery. In this section, we identified Cbx7, which happens to be an essential component of the chromatin modifying machinery, as an epigenetically regulated gene in GBM. We observed from the methylation array carried out in our lab, that Cbx7 was one of the highly methylated genes. We also validated that Cbx7 is downregulated in GBM and the same observation was further corroborated from other data sets. The hypermethylated state of Cbx7 was confirmed by DNA bisulphite sequencing and the expression levels of Cbx7 also got alleviated after 5-Aza-2′-deoxycytidine treatment, which is a DNA methylation inhibitor. This indicated that the down regulation of Cbx7 could be attributed to the methylation of its promoter region. In order to figure out the role of Cbx7 in GBM, we carried out transcriptome analysis of Cbx7 overexpressing cells compared to vector control condition by RNA sequencing. Gene ontology analysis revealed a significant enrichment of pathways involved in cell cycle, migration and invasion like processes. In fact, the exogenous overexpression of Cbx7 leads to cell death, reduced colony formation, retarded migration and invasion of cells. In order to explain the above phenotypes brought about by the exogenous expression of Cbx7, we further examined the RNA sequencing data and observed that many of the top most downregulated genes in Cbx7 overexpression state belonged to the Hippo signaling pathway. The effectors of the Hippo pathway, YAP and TAZ which essentially antagonize the pathway activity, are well known for their role in proliferation, migration and invasion in cancer. So we carried out a Gene Set Enrichment Analysis (GSEA) and found that there was a significant negative enrichment of YAP/TAZ targets in the Cbx7 regulated gene set. We validated some of these targets that were downregulated by Cbx7 overexpression. One of the most downregulated genes that we validated was Connective Tissue Growth Factor (CTGF), which also happens to be a bonafide target of YAP/TAZ. Independent downregulation of CTGF also resulted in reduced migration, thereby phenocopying the effects as were produced by Cbx7 overexpression. Moreover, we also observed that SAPK/JNK was the only kinase whose activity was abolished upon Cbx7 overexpression. Since CTGF is known to activate SAPK/JNK, we assessed the SAPK/JNK activity upon CTGF silencing. We found that levels of phospho-SAPK/JNK were significantly reduced in CTGF silenced condition. In addition to that, the inhibition of the SAPK/JNK by synthetic inhibitor also hampered the migration ability of the cells. We were also able to rescue the loss of migratory potential of glioma cells by the exogenous overexpression of CTGF in Cbx7 stable background. A similar rescue was also achieved by the overexpression of a constitutively active form of SAPK/JNK. This indicates that Cbx7 activates Hippo pathway to inhibit YAP/TAZ dependent transcription, resulting in the downregulation of CTGF, thereby inhibiting CTGF mediated activation of SAPK and thus resulting in the inhibition of glioma cell migration. PART 2: ROLE OF MIRNAS IN GLIOMA DEVELOPMENT AND PROGRESSION miRNAs are a class of small non-coding RNAs that are not translated into functional proteins but still contribute to numerous cellular processes, thereby adding yet another realm of regulation and control. miRNAs bring about gene regulation at the post-transcriptional level, either by degrading the mRNA or by translational repression and in this manner fine tune the expression of protein coding genes. miRNAs are often located in the most fragile sites of the genome which exposes them to grave genetic alterations, thus providing a circumstantial evidence of their etiological role in tumorigenesis. In a malignant state, miRNAs have been found to play pivotal roles in cellular transformation by altering various cellular phenotypes. Owing to their participation in diverse cellular functions, miRNAs have gained a strong foothold in gene regulation. Though a lot has been deciphered about the functional aspect of miRNAs, not much is known about the precise mechanisms which lead to their misregulation and therefore demands in-depth study. The expression of miRNAs can be modulated by a variety of genetic and epigenetic mechanisms. Section I: Role of miR-326 – a PI3 kinase regulated miRNA, in gliomagenesis The TCGA group in the year 2008 identified three major pathways which go disarray in GBM. These include the pro-tumorigenic receptor tyrosine kinase (RTK) pathway, and the p53 and the pRB tumour-suppressive pathways. The RTK signalling includes the PI3 kinase pathway, which is pivotal in gliomagenesis and many other cancers. This directed us to elucidate the set of miRNAs which are controlled by the aberrant functioning of the PI3 kinase pathway. We used synthetic inhibitor LY294002 to abrogate the PI3 kinase signalling and examined the miRNA profile in two glioma cell lines U87 and U251, which have an activated PI3 kinase pathway. Indeed the abrogation of the PI3 kinase pathway resulted in the modulation of a wide array of miRNAs. We validated miR-326 as one of the miRNAs that was upregulated upon PI3 kinase pathway abrogation. Furthermore, we observed that miR-326 was a down regulated miRNA in GBM and different glioma cell lines, as well as in many other publicly available data sets. We also observed that miR-326 is an intragenic miRNA and its host gene Arrestin β1 (ARRB1) also exhibited similar upregulation upon PI3K pathway inhibition. Over-expression of miR-326 resulted in various anti-tumorigenic affects like reduced proliferation, reduced migration and colony suppression. In order to find the targets of miR-326, we analysed the transcriptome by RNA sequencing upon pre-miR-326 transfection. We shortlisted and validated some of the genes which were getting regulated through miRNA over-expression and also explain the functional role of miR-326. Section II: Role of miR-4484 – a copy number deleted miRNA, in gliomagenesis In the TCGA study mentioned above, it was also unfurled that there are many genes in the RTK, p53 and pRB signalling pathways which are made dysfunctional through gene deletions and amplifications. We envisaged whether it is only the protein coding genes which are subjected to such regulations or the non-coding genes like miRNAs as well. In this pursuit, we identified miR-4484 as one of the miRNAs located in the deleted region of uroporphyrinogen III synthase (UROS) gene in the chromosome 11 of the GBM genome. As conceived, miR-4484 was observed to be a downregulated miRNA in association with its host gene UROS. We further elucidated that the downregulation was due to the co-deletion of a locus harbouring both the protein coding gene and the miRNA. In addition, upon over-expression of miR-4484, we observed reduced migration and colony formation, indicating its role as a tumour–suppressor. For seeking the targets of miR-4484, we extracted RNA from miR-4484 over-expression condition and subjected it to RNA sequencing. We shortlisted and validated some of the genes which were getting regulated through miRNA over-expression and possibly explain the functional role of miR-4484.

The Central Dogma of molecular biology describes a framework for how genetic information is transferred in cells, placing RNA as a messenger between DNA and translated proteins. During the last years, interest in RNA research has grown tremendously due to the increasing understanding and recognition of the importance of RNA in regulation of gene expression, biochemical catalysis, and genome integrity surveillance. Most importantly, RNA content, unlike DNA, changes constantly, fine-tuning the cellular response to match the environmental conditions. There is a clear potential for RNA biomarkers, reflecting both the natural and pathological conditions in vivo. Various methods have been developed to study RNA, of which the most common tools and techniques are described in this thesis. Since many of these gold standard methods are based on detecting RNA derivative (cDNA), there is a wide scope for efficient alternative tools directly targeting RNA. In Paper I, the spatiotemporal expression of human adenovirus-5 mRNA in epithelial and blood cells infected with the virus has been studied. For this, padlock probes and rolling circle amplification (RCA) were used to visualize, quantify and analyse both viral and host cell cDNAs in different infection scenarios, at single cell level. In Paper II, direct RNA detection fidelity has been evaluated using padlock probes. A novel type of probe (iLock) that is activated on RNA via invasive cleavage mechanism, prior to RCA was developed in this approach. Using iLocks, a substantial improvement of direct RNA sensing fidelity has been observed. In Paper III, RNA modifications were introduced in otherwise DNA iLock probes to enhance the probes’ efficiency on miRNAs. Using chimeric iLock probes, multiplexed differentiation of conserved miRNA family members were performed with next- generation sequencing-by-ligation readout. Efficient replication of chimeric probes used in Paper III implies that the Phi29 DNA polymerase readily accepts RNA-containing circles as amplification substrates. In Paper IV, real-time RCA monitoring for measurement of amplification rates and analysis of amplification patterns of various RNA-containing circles was achieved. Moreover, the RCA products were sequenced as a proof for the reverse-transcriptase activity of the Phi29 DNA polymerase. This thesis effectively contributes to a better understanding of mechanisms influencing RNA detection with, but not limited to, padlock probes. It expands the available RNA analyses toolkit with novel strategies and solutions, which can be potentially adapted for RNA-focused research, in general and molecular diagnostics, in particular. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

Les cellules cancéreuses sont capables de réactiver la transition Epithélio-Mésenchymateuse (EMT), mécanisme embryonnaire, pour acquérir une mobilité et une capacité de dédifférenciation. L'EMT conduit à une reprogrammation génétique avec la réactivation d'inducteurs de l'EMT, qui sont en majorité des facteurs de transcription (EMT-TF), et conduit à l'inhibition de miARN. Par ailleurs des stress oncogéniques sont essentiels à la progression tumorale. Le but de mon projet de thèse était de comprendre comment les événements de reprogrammation génétique survenant au cours de l'EMT coopèrent avec des stress oncogéniques dans la transformation tumorale mammaire.Premièrement, un criblage basé sur la coopération oncogénique en soft agar assay, entre les EMT-TFs et les stress oncogénique a été réalisé. Suite à une analyse bioinformatique, différentes signatures d'EMT-TF associés à un stress oncogénique ont été identifiées. Ainsi, par exemple, l'expression de l'EMT-TF Zeb1 et l'EMT-TF GSC sont associés à la délétion du gène suppresseur de tumeur PTEN pour transformer des cellules mammaires immortalisées. Une analyse en immuno-histochimie sur un set de 558 tumeurs du sein triple négatives a validé in vivo la présence d'une corrélation entre l'expression de GSC et l'expression de PTEN. Cependant cette association semble être plus complexe. En effet, l'expression de GSC est négativement associée à l'expression nucléaire de PTEN tandis qu'elle est positivement associée à l'expression de PTEN cytoplasmique. Enfin une analyse sur des métadonnées publiques de cancers telles que le TCGA ou le METABRIC est en cours pour valider ces signatures in vitro et plus largement pour déterminer comment l'EMT ou les signatures associées aux EMT-TF se corrèlent avec les voies oncogéniques classiques. Deuxièmement, une analyse in silico à partir d'algorithmes prédictifs de cibles de miARN, a été réalisée pour sélectionner les miARN capables d'inhiber l'expression de plusieurs EMT-TF. Deux miARN (miR-495 et 590-3p) ont été identifiés ciblant plusieurs membres des 4 principales familles d'EMT-TF (FoxC, Snail, bHLH et ZEB). Des tests in vitro ont été réalisés pour valider ces régulations identifiant Slug comme une cible de miR-590-3p. De plus, l'expression de ces miARN dans des lignées cellulaires mammaires est négativement associée à l'expression des EMT-TF et des marqueurs de l'EMT. Un traitement au TGF, inducteur de l'EMT, diminue leur expression, signifiant potentiellement que ces miARN peuvent négativement réguler l'EMT. En parallèle, plusieurs EMT-TF sont capables de réprimer l'expression de miR-590-3p, agissant directement sur son promoteur, créant ainsi des boucles de régulation. Des études fonctionnelles utilisant des vecteurs d'expression stable de miR-590-3p sembleraient montrer un rôle secondaire de ce miARN dans la régulation de l'EMT car mir-590-3p dérégule des marqueurs secondaires de l'EMT comme la N-cadhérine. Des études de restauration de fonctions sont envisagées pour déterminer quelle est l'importance de ces boucles de régulation dans la progression tumorale mammaire. Plus largement, l'expression des miARN identifiés va être corrélée avec les signatures associées aux EMT-TF et aux voies oncogéniques classiques pour déterminer le lien entre ces trois composants dans la tumorigenèse mammaire. Mes travaux de thèse ont montré qu'il existait un intéractome entre des inducteurs de l'EMT, des stress oncogéniques et des miARNs au cours de la transformation mammaire humaine / Cancer cells are able to reactivate the Epithelio-Mesenchymal Transition (EMT), an embryonic mechanism, to acquire mobility and dedifferentiation capacities. EMT leads to a genetic reprogramming with the reactivation of EMT inductors, mainly transcription factors (EMT-TF) and the inhibition of miRNA. Otherwise, oncogenic stresses are essentials to tumor progression. The aim of my thesis project was to have a better understanding about the cooperation between events of genetic reprogramming occurring during EMT and oncogenic stresses during mammary tumor transformation. First, a screening based on oncogenic cooperation in soft agar assay, between EMT-TFs and oncogenic stresses was performed. Following a bioinformatics analysis, different EMT-TFs signatures associated with an oncogenic stress were identified. Thus, for example, the expression of EMT-TF ZEB1 and GSC were associated with the deletion of tumor suppressor gene PTEN to transform immortalized mammary epithelial cells. An immunohistochemistry analysis on a set of 558 triple negative breast cancers validated in vivo the presence of a correlation between the expressions of GSC and PTEN. However, this association seems to be more complex. Indeed, the expression of GSC is negatively associated with the nuclear expression of PTEN while it’s positively associated with the cytoplasmic expression of PTEN. Finally, an analysis of public metadata on cancer samples as TCGA or METABRIC is ongoing to validate these in vitro signatures and wider to determine how EMT or EMT-TFs associated signatures correlate with classical oncogenic pathways.Secondly, an in silico analysis, from predictive algorithms of miRNA targets, was performed to select miRNA able to inhibit the expression of several EMT-TFs. Two miRNA (miR-495 and miR-590-3p) were identified targeting several members of four principal’s families of EMT-TFs (FOXC, Snail, bHLH and ZEB). In vitro tests were realized to validate these regulations identifying Slug as a target of miR-590-3p. Moreover, these miRNAs expression in mammary cell lines is negatively correlated with EMT-TFs expression and EMT markers. A treatment with TGF-, a major EMT inductor, decreases their expression, potentially meaning that these miRNA can negatively regulate EMT. In parallel, several EMT-TFs are able to repress the expression of miR-590-3p, acting directly on its promotor, thus creating feedback loops. Functional studies using stable expression vector of miR-590-3p suggest a secondary role of this miRNA in the regulation of EMT because miR-590-3p deregulates EMT secondary markers as N-Cadherin. Functions restauration studies are planned to determine how important these feedback loops in mammary tumor progression are. To open the project, expression of these identified miRNA will be correlated with EMT-TF associated signatures and with classical oncogenic pathways to determine the link between these three components in mammary tumorigenesis. My thesis works are shown that there is an interactome between EMT inductors, oncogenic stresses and miRNA during human mammary transformation

Le rétrovirus HTLV-1 (Human T-cell Leukemia virus type 1) est l'agent étiologique de la leucémie T de l'adulte (ATLL) et de maladies inflammatoires. Il infecte principalement les lymphocytes T-CD4+ et T-CD8+, et se réplique essentiellement via l'expansion clonale de sa cellule hôte selon deux mécanismes distincts : HTLV-1 induit une résistance à l'apoptose des cellules T-CD8+ alors qu'il favorise la prolifération des cellules T-CD4+. Au stade chronique de l'infection, en comparaison à leur contreparties T-CD8+, les cellules T-CD4+ infectées non transformées présentent des caractéristiques pré-leucémiques telles que des anormalités génomiques et des défauts d'activation de la télomérase, ce qui explique vraisemblablement pourquoi les cellules d'ATLL sont régulièrement de phénotype T-CD4+. L'infection par HTLV-1 s'accompagne de reprogrammations drastiques du transcriptome cellulaire. Parmi elles, les modifications d'expression de micro-ARN (miARN). Les miARN sont de petits ARN non-codants qui contrôlent négativement la traduction des ARNm, et qui ont été récemment mis en évidence dans les cellules transformées par le virus, et semblent participer au maintien du phénotype tumoral. Ces données posent la question de l'origine de ces perturbations et de leurs implications dans les processus d'expansion clonale et d'initiation de la transformation des cellules infectées. Pour adresser cette question, nous avons réalisé une étude intégrée de l'expression des miARN et des ARNm de cellules T, issues de patients infectés sans malignité / Human T-cell leukemia virus type 1 (HTLV-1) is associated with adult T-cell leukemia / lymphoma (ATLL) hat regularly occurs after a prolonged period of viral latency. In vivo, HTLV-1 replication relies on the clonal expansion of its host CD4+ and CD8+ T-cells, yet the virus causes adult T-cell leukemia / lymphoma (ATLL) that is regularly of the CD4+ phenotype. Infected cells express Tax and HBZ viral oncoproteins. Tax is mainly expressed in untransformed cells, where it promotes cell proliferation, genetic instability, and miRNA dysregulation, whereas HBZ is expressed in both untransformed and malignant T-cells where it contributes to promote cell proliferation and to silence virus expression. Here, we show that an HBZ / miRNA axis promotes cell proliferation and genetic instability. MicroRNAs (miRNAs) are evolutionarily conserved, small (~21 nucleotides), noncoding RNAs that are encoded within the genomes of almost all eukaryotes from plants to mammals. In general, miRNAs, especially in animals, post-transcriptionally regulate protein synthesis by base pairing to partially complementary sequences in the 3’ untranslated regions (UTRs) of target mRNAs. Furthermore, whereas human lymphocyte subsets are known to possess specific miRNA signatures involved in T-cell differentiation and activation, little is known about the role of miRNA dysregulation in the clonal expansion of untransformed, infected CD4+ and CD8+ T-cells in vivo, including its role, if any, in viral persistence, inflammation, genetic instability, and early leukemogenesis. To our knowledge, no study to date has assessed the effects of HBZ on the biogenesis and activity of miRNAs. In order to assess the effect of HTLV-1 infection on the miRNA expression profiles of host cells in vivo, we performed an integrated analysis of miRNA- and mRNA-expression profiles of cloned CD4+ and CD8+ T-cells derived from infected individuals without malignancy

Nicotine dependence is responsible for perpetuating the adverse health effects due to tobacco use, the leading cause of preventable death worldwide. Nicotine is an agonist for nicotinic acetylcholine receptors, which are enriched in the mesocorticolimbic and habenulo-interpeduncular circuitries, underlying nicotine reward and withdrawal, respectively. Drugs of abuse, including nicotine, induce stable neuroadaptations, requiring protein synthesis through regulation of transcription factors, epigenetic mechanisms, and non-coding RNAs. It also been shown that miRNAs in brain are regulated by nicotine and that miRNA dysregulation contributes to brain dysfunction, including drug addiction. While much is known about the neurocircuitry responsible for the behaviors associated with nicotine reward or withdrawal, the underlying molecular mechanisms of how these changes in behavior are induced are less clear. Using miRNA-/mRNA-Seq, we demonstrate that there are widespread changes in both miRNA and mRNA expression in brain regions comprising the mesocorticolimbic circuit after chronic nicotine treatment, and the habenulo-interpeduncular circuit during acute nicotine withdrawal. Conserved, differentially expressed miRNAs were predicted to target inversely regulated mRNAs. We determined that expression of miR-106b-5p is up-regulated and Profilin 2 (Pfn2), an actin-binding protein enriched in the brain, is down-regulated in the interpeduncular nucleus (IPN) during acute nicotine withdrawal. Further we show that miR-106b-5p represses Pfn2 expression. We demonstrate that knockdown of Pfn2 in the IPN is sufficient to induce anxiety, a symptom of withdrawal. This novel role of Pfn2 in nicotine withdrawal-associated anxiety is a prime example of this dataset’s utility, allowing for the identification of a multitude of miRNAs/mRNA which may participate in the molecular mechanisms underlying the neuroadaptations of nicotine dependence.

No description available.

Children descending from pregnancy complicated by gestational hypertension, preeclampsia or fetal growth restriction have a lifelong increased risk of development of cardiovascular disease. This study investigates the expression profile of 29 cardiovascular and cerebrovascular microRNAs in children at the age of 3 to 11 years. MicroRNAs are short non-coding RNA molecules affecting gene expression by posttranscriptional modifications of mRNA, which affects biological processes. Abnormal microRNA levels can lead to pathological conditions of the individual. This study explores the relationship between dysregulated microRNA levels in whole peripheral venous blood of children and the presence of complications during pregnancy. Furthermore, this study looks at expression profile specificities depending on the presence of pathology in the child's cardiovascular system, as found in a clinical examination consisting of BMI assessment and evaluation, blood pressure testing and ultrasound examination of the heart. Dysregulated profile was present in children with gestational hypertension in miR-1-3p, miR-17-5p, miR-20a-5p, miR-21-5p, miR-26a-5p, miR-29a-3p, miR-126-3p, miR-133a-3p, miR-181a-5p, miR-199a-5p, miR-342-3p and miR-499-5p. In children with preeclampsia, dysregulation was found with miR-1-3p and...

Background: Recently high-throughput sequencing (HTS) using next generation sequencing techniques became useful in digital gene expression profiling. Our study introduces analysis options for HTS data based on mapping to miRBase or counting and grouping of identical sequence reads. Those approaches allow a hypothesis free detection of miRNA differential expression. Methods: We compare our results to microarray and qPCR data from one set of RNA samples. We use Illumina platforms for microarray analysis and miRNA sequencing of 20 samples from benign follicular thyroid adenoma and malignant follicular thyroid carcinoma. Furthermore, we use three strategies for HTS data analysis to evaluate miRNA biomarkers for malignant versus benign follicular thyroid tumors. Results: High correlation of qPCR and HTS data was observed for the proposed analysis methods. However, qPCR is limited in the differential detection of miRNA isoforms. Moreover, we illustrate a much broader dynamic range of HTS compared to microarrays for small RNA studies. Finally, our data confirm hsa-miR-197-3p, hsa-miR-221-3p, hsa-miR-222-3p and both hsa-miR-144-3p and hsa-miR-144-5p as potential follicular thyroid cancer biomarkers. Conclusions: Compared to microarrays HTS provides a global profile of miRNA expression with higher specificity and in more detail. Summarizing of HTS reads as isoform groups (analysis pipeline B) or according to functional criteria (seed analysis pipeline C), which better correlates to results of qPCR are promising new options for HTS analysis. Finally, data opens future miRNA research perspectives for HTS and indicates that qPCR might be limited in validating HTS data in detail.:Background; Methods; Results; Discussion; Conclusions