>Magister Scientiae - MSc / Systemic lupus erythematosus is a chronic, inflammatory disease characterised by the production of autoantibodies which target particularly the nuclear components of multiple cell types throughout the body. MicroRNA’s have been well-established to regulate gene function by partial-, or complete binding to the 3’-UTR of the target genes, causing repression or complete degradation of the target gene. As a result, proteins normally produced by the targeted mRNA would exhibit a decrease in production.The aim of this study was to investigate the interactions between genes and microRNAs implicated in the pathogenesis of SLE. Objectives included curating lists of miRNAs and genes associated with lupus pathogenesis, to identify regulatory targets of miRNAs and genes targeted by miRNAs, and to find the intersections of these outputs. By examining the intersections of the resultant targets, we aimed to identify novel interactions using Pathway Analysis, which have not been previously reported in scientific literature, to be associated with the pathogenesis of SLE. Understanding the miRNA-gene target interactions in the progression of SLE may provide us with essential biomarkers and targets for disease diagnosis and therapy. / National Research Foundation (NRF) and DAAD

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No / Hair follicle development and its postnatal regeneration are characterized by dramatic changes in its microanatomy and cellular activity, which are controlled by multiple signalling pathways, transcription factors and epigenetic regulators, including microRNAs (miRNAs). miRNAs and their targets form remarkably diverse regulatory networks, playing a key role in the execution of gene expression programmes in the different cell lineages of the hair follicle. This review summarizes the roles of miRNAs in the control of hair follicle development, cycling and hair pigmentation, emphasizes the remaining problems/unanswered questions, and provides future directions in this rapidly growing and exciting area of research / MRC

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the production and deposition of nuclear self-antigen-containing immune complexes. Epigenetic factors, including altered microRNA (miRNA) expression, may contribute to aberrant immune cell function in SLE. miRNAs are small, noncoding RNAs that bind to the 3’ untranslated region of target mRNAs resulting in post-transcriptional gene modulation. IL-6, an inflammatory cytokine overproduced by mesangial cells in SLE, contains a potential binding site for miR-let-7a. In order to examine if alterations in miR-let-7a expression can influence inflammatory mediator production in SLE, we isolated mesangial cell miRNAs from 8 and 32- week-old female New Zealand Black/White (NZB/W) mice. We found miR-let-7a expression was significantly increased in the mesangial cells of pre-diseased and actively diseased NZB/W mice compared to age-matched female New Zealand White (NZW) controls. Overexpression of miR-let-7a in vitro increased IL-6 production in LPS/IFN-γ-stimulated mesangial cells compared to the stimulated control. Due to the crucial role of miR-let-7a in cell division and inflammation, we investigated miR-let-7a-mediated proliferation and NFκB activation in J774A.1 macrophages and MES 13 mesangial cells in vitro. Cell proliferation, retinoblastoma protein (Rb) phosphorylation, and NFκB activation were increased in cells transfected with miR-let-7a and stimulated with LPS/IFN-γ. Expression and production of the cell cycle inhibitor E2F5 was decreased in stimulated cells overexpressing miR-let-7a. We found that the cell cycle promoter E2F2 and NFκB target the miR-let-7a promoter. Next we sought to determine alterations in iii specific disease-associated miRNAs in female NZB/W mice treated with hydroxychloroquine (HCQ) or prednisone (PRED) for 12 weeks beginning at 20 weeks-of-age. We found that treatment with HCQ or PRED induced unique changes to miRNA expression in multiple tissues. In order to identify specific miRNAs as disease-modifying agents and not merely disease correlates, further in vitro analyses confirmed HCQ or PRED-mediated inhibition of miRNAs is critical to alter the inflammatory response. Taken together, our results suggest that overexpression of miR-let-7a may contribute to hyperplasia and the proinflammatory response in SLE. Our studies indicate that lupus therapeutics may work, in part, by altering the expression of disease-associated miRNAs in immune cells and the urine. / Ph. D.

Polimorfismos de um nucleotídeo (SNPs) podem alterar, além de códons de leitura da tradução de genes, posições genômicas importantes do processo de regulação gênica, como sítios de iniciação de transcrição, de splicing e, mais especificamente, sítios alvos de microRNAs (miRNAs). Em parti- cular, a identificação de SNPs alterando sítios alvos de miRNAs é um problema em aberto, embora venha ganhando um importante destaque nos últimos anos decorrente dos avanços descobertos sobre a capacidade dos miRNAs como elementos reguladores do genoma, associados inclusive a muitas doenças como o câncer e vários transtornos psiquiátricos. Os recursos computacionais atualmente disponíveis para esta finalidade (alguns bancos de dados e uma ferramenta) estão restritos à análise de SNPs na região 3UTR (UnTranslated Regions) de RNAs mensageiros, onde miRNAs geralmente se ligam para reprimir sua tradução. No entanto, essa é uma simplificação do problema, dado que já se conhece a regulação por miRNAs ativando ou reprimindo a transcrição gênica quando ligados à sua região promotora, aumentando a efetividade da regulação negativa da tradução quando ligados à região codificante do gene ou ainda miRNAs se ligando a RNAs não codificantes. Esses recursos se limitam também à identificação de SNPs na região seed dos sítios de miRNAs, e portanto só identificam criação ou ruptura de sítios. Porém, SNPs localizados fora dessa região não só podem colaborar na criação e ruptura de sítios como também interferir na estabilidade de ligação de miRNAs e, por- tanto, na efetividade da regulação. Além disso, considerando toda a extensão do sítio, não somente a seed , é possível ocorrer mais de um SNP e, sendo assim, a combinação desses SNPs pode ter uma influência ainda maior na ligação com o miRNA. Os recursos atuais também não informam quais alelos dos SNPs, muito menos quais combinações deles, estão causando qual efeito. Por fim, tais recursos estão restritos a Homo sapiens e Mus musculus. Assim, este trabalho apresenta a ferramenta computacional SIMTar (SNPs Interfering in MicroRNA Targets), desenvolvida para identificar SNPs que alteram sítios alvos de miRNAs e que preenche as lacunas mencionadas. Além disso, é descrita uma aplicação de SIMTar na análise de 114 SNPs associados à esquizofrenia, na qual todos foram preditos interferindo em sítios alvos de miRNAs. / Single nucleotide polymorphisms (SNPs) can be involved in alteration of not only open reading frame but also important genomic positions of gene regulation process such as transcription initiation sites, splicing sites and microRNA target sites. In particular, the identification of SNPs interfering on microRNA target sites is still an open problem, despite its increasing prominence in recent years due to the discoveries about the microRNA abilities as regulatory elements in the genome and association with severals diseases such as cancer and psychiatric disorders. The computational resources currently available for this purpose (four databases and one tool) are restricted to the analysis of SNPs in the 3UTR (UnTranslated Regions) of mRNAs, where the microRNAs typically bind in order to repress their translation. However, this is a simplification of the problem, since it is already known the gene transcription activation by microRNAs bound to its promoter region, increasing of the effectiveness of negative regulation of translation when microRNAs are bound to the coding region of the gene or binding of microRNA into non-coding RNAs. These resources are also limited to the identification of SNPs in the seed region of miRNAs, and therefore they can only identify sites creation or disruption. However, SNPs located outside this region can not only create and disrupt target sites but also interfere on the stability of miRNAs binding and therefore on the regulation effectiveness. Moreover, considering the target site length, more than one SNP can occur inside of a site and thus, the combination of these SNPs can have an even greater influence on the microRNA binding. Also, current resources do not display which alleles of SNPs or what combinations of them are causing which effect. Finally, these features are restricted to the Homo sapiens and Mus musculus species. This work presents the computational tool SIMTar (SNPs Interfering on MicroRNA Targets), developed to identify SNPs that alter miRNA target sites and fills the mentioned gaps. Finally, it is described an application of SIMTar on the analysis of 114 SNPs associated with schizophrenia, all of them being predicted interfering with miRNA target sites.

Polimorfismos de um nucleotídeo (SNPs) podem alterar, além de códons de leitura da tradução de genes, posições genômicas importantes do processo de regulação gênica, como sítios de iniciação de transcrição, de splicing e, mais especificamente, sítios alvos de microRNAs (miRNAs). Em parti- cular, a identificação de SNPs alterando sítios alvos de miRNAs é um problema em aberto, embora venha ganhando um importante destaque nos últimos anos decorrente dos avanços descobertos sobre a capacidade dos miRNAs como elementos reguladores do genoma, associados inclusive a muitas doenças como o câncer e vários transtornos psiquiátricos. Os recursos computacionais atualmente disponíveis para esta finalidade (alguns bancos de dados e uma ferramenta) estão restritos à análise de SNPs na região 3UTR (UnTranslated Regions) de RNAs mensageiros, onde miRNAs geralmente se ligam para reprimir sua tradução. No entanto, essa é uma simplificação do problema, dado que já se conhece a regulação por miRNAs ativando ou reprimindo a transcrição gênica quando ligados à sua região promotora, aumentando a efetividade da regulação negativa da tradução quando ligados à região codificante do gene ou ainda miRNAs se ligando a RNAs não codificantes. Esses recursos se limitam também à identificação de SNPs na região seed dos sítios de miRNAs, e portanto só identificam criação ou ruptura de sítios. Porém, SNPs localizados fora dessa região não só podem colaborar na criação e ruptura de sítios como também interferir na estabilidade de ligação de miRNAs e, por- tanto, na efetividade da regulação. Além disso, considerando toda a extensão do sítio, não somente a seed , é possível ocorrer mais de um SNP e, sendo assim, a combinação desses SNPs pode ter uma influência ainda maior na ligação com o miRNA. Os recursos atuais também não informam quais alelos dos SNPs, muito menos quais combinações deles, estão causando qual efeito. Por fim, tais recursos estão restritos a Homo sapiens e Mus musculus. Assim, este trabalho apresenta a ferramenta computacional SIMTar (SNPs Interfering in MicroRNA Targets), desenvolvida para identificar SNPs que alteram sítios alvos de miRNAs e que preenche as lacunas mencionadas. Além disso, é descrita uma aplicação de SIMTar na análise de 114 SNPs associados à esquizofrenia, na qual todos foram preditos interferindo em sítios alvos de miRNAs. / Single nucleotide polymorphisms (SNPs) can be involved in alteration of not only open reading frame but also important genomic positions of gene regulation process such as transcription initiation sites, splicing sites and microRNA target sites. In particular, the identification of SNPs interfering on microRNA target sites is still an open problem, despite its increasing prominence in recent years due to the discoveries about the microRNA abilities as regulatory elements in the genome and association with severals diseases such as cancer and psychiatric disorders. The computational resources currently available for this purpose (four databases and one tool) are restricted to the analysis of SNPs in the 3UTR (UnTranslated Regions) of mRNAs, where the microRNAs typically bind in order to repress their translation. However, this is a simplification of the problem, since it is already known the gene transcription activation by microRNAs bound to its promoter region, increasing of the effectiveness of negative regulation of translation when microRNAs are bound to the coding region of the gene or binding of microRNA into non-coding RNAs. These resources are also limited to the identification of SNPs in the seed region of miRNAs, and therefore they can only identify sites creation or disruption. However, SNPs located outside this region can not only create and disrupt target sites but also interfere on the stability of miRNAs binding and therefore on the regulation effectiveness. Moreover, considering the target site length, more than one SNP can occur inside of a site and thus, the combination of these SNPs can have an even greater influence on the microRNA binding. Also, current resources do not display which alleles of SNPs or what combinations of them are causing which effect. Finally, these features are restricted to the Homo sapiens and Mus musculus species. This work presents the computational tool SIMTar (SNPs Interfering on MicroRNA Targets), developed to identify SNPs that alter miRNA target sites and fills the mentioned gaps. Finally, it is described an application of SIMTar on the analysis of 114 SNPs associated with schizophrenia, all of them being predicted interfering with miRNA target sites.

Ovarian cancer results from the dysregulation, in normal ovarian epithelial cells, of genes responsible for the control of critical biological processes. Since their discovery 20 years ago, microRNAs have increasingly been implicated in that dysregulation due to their role mediating gene expression; changes in microRNA expression levels in cancer have been linked with tumor growth, proliferation and metastasis. Their imputed involvement in cancer has led to the possibility of their use as biomarkers and to their potential clinical use. Using mRNA and microRNA microarray analysis to compare human gene expression in normal ovarian surface epithelial (OSE) cells and epithelial ovarian cancer (EOC) cells, we explored the interactions between microRNAs and genes. First, we validated in silico predictions of microRNA targets by comparing them with in vitro evidence after exogenous microRNA transfection. We found that pairs of microRNAs with identical 7-nt (nucleotide) seed regions shared 88% of their predicted targets and 55% of their in vitro targets, confirming the importance of the seed as a targeting mechanism. But more importantly, we found that even a single nucleotide change in the seed region can result in a significant shift in the set of targeted genes, implying strong functional conservation of the seeds and their corresponding binding sites. Next, we discovered a 3-element network motif which explains the upregulation of nearly 800 genes in ovarian cancer which, as predicted microRNA targets, might be expected to be down- regulated. This model shows that, under certain circumstances, repressor genes which are down- regulated in cancer can apparently override the repressive effects of microRNAs, resulting in the upregulation of predicted microRNA targets. Finally, we developed a phenomenological network model, based on the Pearson correlation of microarray gene expression data, to identify subnetworks dysregulated in cell cycle and apoptosis. While our methodology reported many genes previously associated with ovarian cancer, it significantly suggested potentially oncogenic genes for further investigation. This network model can easily be extended to identify dysregulated genes in other cancers.

We have hypothesized that dietary modulation of intestinal miRNA expression may contribute to the chemoprotective effects of nutritional bioactives (fish oil and pectin). Using a rat colon carcinogen model, we determined miRNAs-let-7d, miR-15b, miR-107, miR-191 and miR-324-5p were modulated by fish oil + pectin. We also demonstrated that BACE1 and PTEN are targets of miR-107 and miR-21, respectively. To further elucidate the biological effects of diet and carcinogen on miRNAs, we integrated global miRNAs, total and polysomal gene expression datasets obtained from the above mentioned study and used four computational approaches. We demonstrated that polysomal profiling is tightly related to microRNA changes when compared with total mRNA profiling. In addition, diet and carcinogen exposure modulated a number of microRNAs and complementary gene expression analyses showed that oncogenic PTK2B, PDE4B, and TCF4 were suppressed by the chemoprotective diet at both the mRNA and protein levels. To determine the function of select diet and colon carcinogen modulated miRNAs and to validate their targets, we carried out a series of loss and gain of function experiments along with luciferase reporter assays. We verified that PDE4B and TCF4 are direct targets of miR-26b and miR-203, respectively. PTK2B was determined to be an indirect target of miR-19b. In addition, microRNA physiological function was assessed by examining effects on apoptosis and cell proliferation. To better understand how the colonic stem cell population responds to environmental factors such as diet and carcinogen, we investigated the chemoprotective effects of dietary agents on miRNAs in colonic stem cells obtained from Lgr5-EGFP-IRES-creERT2 knock in mice injected with AOM. We demonstrated that based on relative expression of miR-125a-5p, miR-190b and miR-191 in stem cells vs. daughter cells and differentiated cells, these miRNAs may be stem cell specific miRNAs. We also identified miR-21 to be significantly reduced in stem cells compared to differentiated cells and selectively modulated by these dietary agents in stem cells. In summary, our results indicate for the first time that fish oil plus pectin protect against colon tumorigenesis in part by modulating a subset of miRNAs and their target genes (mRNAs) implicated in the regulation of the colon stem cell niche and tumor development.

Helicobacter pylori is a gram-negative bacterium that infects half the world population and is the etiological cause of numerous gastric pathologies. H. pylori possess numerous mechanisms to promote its survival and modulate host immunity. We propose that H. pylori can modulate intercellular communication by manipulating the host exosome pathway. Exosomes are secreted nanovesicles that contain different proteins and microRNAs that can be transferred between cells to alter cell signaling and gene expression. We demonstrate that H. pylori infection increases host exosome secretion. Furthermore, infection can alter exosome composition as VacA, a bacterial virulence factor, can be exported in exosomes and Argonaute 5, a miRNA effector protein, is upregulated in exosomes during infection. Lastly, we show preliminary evidence that infection-modulated exosomes can modulate immune-regulatory signaling in dendritic cells by activating STAT3. Together, these studies elucidate a novel mechanism by which H. pylori can modulate the host environment and promote its continued survival.

The last decade has seen considerable research focusing on understanding the factors underlying schizophrenia and bipolar disorder. A major challenge encountered in studying these disorders, however, has been the contribution of genetic, or etiological, heterogeneity to the so-called “missing heritability” [1-6]. Further, recent successes of large-scale genome-wide association studies (GWAS) have nonetheless seen only limited advancements in the delineation of the specific roles of implicated genes in disease pathophysiology. The study of microRNAs (miRNAs), given their ability to alter the transcription of hundreds of targeted genes, has the potential to expand our understanding of how certain genes relate to schizophrenia and bipolar disorder. Indeed, the strongest finding of one recent mega-analysis by the Psychiatric GWAS consortium (PGC) was for a miRNA, though little can be said presently about its particular role in the etiologies of schizophrenia and bipolar disorder [52]. Next generation sequencing (NGS) is a versatile technology that can be used to directly sequence either DNA or RNA, thus providing valuable information on variation in the genome and in the transcriptome. A variation of NGS, MicroSeq, focuses on small RNAs and can be used to detect novel, as well as known, miRNAs [26,125, 126]. The following thesis describes the role of miRNAs in schizophrenia and bipolar disorder in various experimental settings. As an index of the interaction between multiple genes and between the genome and the environment, miRNAs are great potential biomarkers for complex disorders such as schizophrenia and bipolar disorder.