Thesis (MSc (Biomedical Sciences))--Cape Peninsula University of Technology, 2018. / Background: Early detection of individuals who are at risk of developing Glucose Intolerance would decrease the morbidity and mortality associated with this disease. MicroRNA is one of the most widely studied biomolecules involved in epigenetic mechanisms, hence it offers unique opportunities in this regard. Circulating microRNAs are associated with disease pathogenesis during the asymptomatic stage of disease. This has therefore attracted a lot of attention as a potential biomarker for identifying individuals who have an increased risk of developing Glucose Intolerance. The identification of high risk biomarkers for Glucose Intolerance will go a long way to eliminate the possible complications that arise due to late diagnosis and treatment of Glucose Intolerance. This could ultimately lead to better ways to prevent, manage and control the Glucose Intolerance epidemic that is rampant worldwide. The aim of the study is to investigate expression of circulating microRNA’s in blood of mixed ancestry subjects with glucose intolerance. Methods: A quantitative cross-sectional study design involving 36 individuals [who were age, gender and BMI (Body Mass Index) matched] from a total population of 1989 participants of mixed ancestry descent, residing in Bellville South, South Africa was used. Participants were classified as controls (normoglycemic), pre-diabetic (preDM) and diabetic (DM) (screen detected diabetic) according to WHO criteria of 1998. MicroRNAs were extracted from serum using the Qiagen miRNeasy Serum/Plasma Kit (ThermoFisher). The purified micro RNAs were reverse-transcribed to cDNA (complementary deoxyribonucleic acid) using the Qiagen RT2 First Strand Kit. Then, using Qiagen miScript SYBR Green PCR kit and miScript miRNA PCR arrays (ThermoFisher), the real time polymerase chain reaction was done to determine the expression profile the circulating micro RNAs present in the serum of the participants. Results: The 36 participants were evenly divided into 3 groups of 12 participants each as mentioned earlier. There were significant differences between groups in the waist (cm) (p=0.0415) and waist/hip ratio (p=0.0011) with highest values in the DM group and lowest in the normal group. Clinical parameters varied significantly according to glycemic status. As expected, the FBG (mmol/L) (p<0.0001), 2 HRs Post Glucose (mmol/L) (p<0.0001), HbA1c (%) (p=0.0009), Fasting Insulin (mIU/L) (p=0.0039), were all highest in the DM and lowest in the control group. In contrast, the 2 HRs Post Insulin (mIU/L) (p = 0.0027) was highest in the preDM group and lowest in the normal group, while the Glucose/Insulin ratio (p=0.0477) was highest in the normal group and lowest in the preDM group. Triglycerides (mmol/L) (p=0.0043) and Total Chol (mmol/L) (p=0.0429) were significantly increased through the three groups, with highest values in the DM group and lowest in the normal group. Furthermore, 12 of the 84 miRNAs studied were expressed through all the 3 groups and they exhibited both inverse and positive correlations between the clinical parameters, especially the glucose parameters (Fasting blood glucose, 2 hours post glucose, Fasting blood insulin, 2 hours post insulin and Glycated Hemoglobin).

<div>The human ether-a-go-go-related gene (hERG, KCNH2) potassium channel has been implicated in diverse physiological and pathological processes. The KCNH2 gene encodes a rectifier voltage-gated potassium channel (Kv 11.1) that governs the chief repolarizing current, IKr, which is essential for normal electrical activity in excitable cells such as cardiomyocytes. It is also involved in cell growth and apoptosis regulation in non-excitable cells, such as tumor cells. Dysfunction of hERG is associated with potentially lethal complications, including diseases and sudden death under certain circumstances. While the mechanisms regulating KCNH2 expression remain unclear, recent data suggested that microRNAs (miRNAs) are involved, particularly in the context of several pathologic effects. </div><div>miRNA is a class of RNA defined by its conserved, short, non-coding nature. miRNAs are important regulators of gene expression at the post-transcriptional level that bind through complimentary annealing to the 3’ untranslated regions (3’ UTRs) of target mRNAs, resulting in mRNA destabilization and translational repression. The primary objectives of this research were to 1) identify miRNAs regulating KCNH2 expression in cancer, 2) investigate the potential association between miR-362-3p expression and risk of drug-induced QT interval lengthening, and 3) identify miRNAs potentially regulating KCNH2 expression and function in cardiac cells. </div><div>Through bioinformatics approaches, five miRNAs were identified to potentially regulate KCNH2 expression and function in breast cancer cells. The five identified miRNAs were validated through a Dual-Luciferase Assay using the KCNH2 3′ UTR. Only miR-362-3p was validated to bind to the KCNH2 3’ UTR, decreasing luciferase activity by 10% ± 2.3 (P < 0.001, n = 3) when compared to cells transfected with luciferase plasmid alone. miR-362-3p was also the only miRNA that its expression positively correlated with overall survival of patients with breast cancer from The Cancer Genome Atlas-Cancer Genome (TCGA) database by log-rank test (HR: 0.39, 95% CI: 0.18 to 0.82, P = 0.012). Cell proliferation was assessed by MTS assay (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) 48 hours following transfection in breast cancer cell lines, including SK-BR-3 and MCF-7. miR-362-3p significantly decreased proliferation of SK-BR-3 and MCF-7 cells by 23% ± 8.7 (P = 0.014, n = 3) and 11.7% ± 1.0 (P < 0.001, n = 3), respectively. Cell cycle phases in SK-BR-3 and MCF-7 cells were differentiated by flow cytometry 48 hours following transfection. miR-362-3p and hERG siRNA (positive control) significantly increased the accumulation of cells in G0/G1 phase in MCF-7 by 11.7% (from 51.1% ± 0.64 to 57.1 ± 0.96, P = 0.002, n = 3) and 10% (from 51.1% ± 0.64 to 56.8 ± 0.96, P < 0.001, n = 3), respectively. </div><div>The demonstrated ability of miR-362-3p to regulate hERG in breast cancer cells coupled with previously published data that indicated an alteration of miR-362-3p expression during HF and a potential association between its expression and QT interval prolongation suggesting an important role for this miRNA in regulation of hERG function during HF. Therefore, the contribution of miR-362-3p to hERG function was investigated in patients administered the QT prolonging drug ibutilide, known to inhibit hERG. A total of 22 patients completed a prospective, parallel-group comparative study during which they received subtherapeutic doses (0.003 mg/kg) of ibutilide. The study was originally designed to investigate the influence of heart failure with preserved ejection fraction (HFpEF) on response to drug-induced QT prolongation. Blood for determination of serum Ibutilide concentrations and miR-362-3p expression, along with electrocardiograms (ECGs) were serially collected over a span of 12 hours. ΔΔ-Fridericia-heart rate corrected QT (ΔΔ QTF) intervals were utilized for all analyses to account for baseline and diurnal variation. </div><div>To assess the ability of miR-362-3p to predict ibutilide QT-induced ΔΔQTF changes, nonlinear mixed effects pharmacokinetic/ pharmacodynamic (PKPD) modeling was performed to assess the contribution of miR-362-3p to drug-induced QT interval lengthening. The model that best fit serum ibutilide concentrations versus time was a 3-compartment model with first order elimination and proportional residual errors, while the model that best described the ibutilide concentration- ΔΔQTF relationship was an Emax model with an effect compartment. In addition to miR-362-3p expression, several demographic and clinical data were evaluated as potential covariates on PK and PD parameter estimates. Of tested covariates, heart failure (HF) status on Emax (ΔOFV = -4.1; P < 0.05), and miR-362-3p expression on EC50 (ΔOFV = -9.9; P < 0.05) were incorporated in the final PKPD model. The mean individual Emax was significantly higher in HF patients when compared to non-HF patients (P = 0.015), while EC50 was negatively correlated with miR-362-3p expression (P < 0.0001, R2 0.93). </div><div>Previous evidence indicates that miR-362-3p is altered in patients with HF. In addition, several miRNAs commonly regulate the same ion channel. Therefore, we have developed a large-scale high-throughput bioassay (HT-bioassay) to explore and identify other miRNAs potentially involved in KCNH2 expression and function in human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) during sustained β-adrenergic receptor (βAR) stimulation or overexpression of activated calcium/calmodulin-dependent protein kinase 2 (CaMKII), which are classical consequences of HF. </div><div>Through bioinformatic approaches, putative miRNA binding sites (n=327) were identified in the KCNH2 3′ UTR. Fragments containing these putative binding sites were synthesized, cloned into linearized plasmids, and amplified. The plasmid pool was transfected into hiPS-CM cells either treated with βAR stimulation or overexpressing CaMKII. Next-generation sequencing was performed to identify: 1) expression of putative miRNA binding sites and 2) endogenous miRNAs versus control. Eight predicted binding sites were found to be significantly downregulated in the CAMKII group (P <0.05, log fold change -0.287 to -0.59), and six significantly downregulated in the sustained βAR group (P <0.05, log fold change -0.29 to -0.72). Two binding sites were significantly reduced in both treatment groups (P < 0.05, log fold change between -0.38 and -0.61).</div><div>Thirty-one miRNAs were predicted to bind to the 16 binding sites identified from the bioassay. Of these, seven were selected for further screening using dual luciferase assays. None of the putative miRNAs reduced luciferase activity. However, hERG expression was assessed by immunoblot analysis following transfection of the seven miRNAs into HEK293 cells stably expressing hERG (HEK293-hERG). Six of the seven miRNA mimics reduced hERG protein expression. An additional validation step was performed by assessing hERG-related current density by whole cell electrophysiology, in which three of the six miRNAs inhibited hERG protein transfected into HEK293-hERG cells. Those same three miRNA mimics significantly decreased Ikr current (P <0.05). </div><div>Finally, expression of the miRNAs identified by HT-bioassay was examined in the patients enrolled in the clinical trial in which genome-wide next generation sequencing was performed on miRNAs extracted from whole blood samples. Of the 31 miRNAs identified from HT-bioassay, six were found to be expressed in patients (n = 12). A correlation analysis was performed between levels of the expressed miRNAs and corresponding QTF interval lengthening with ibutilide. Of the six miRNAs, only miR-4665-5p was significantly associated with QTF interval (P = 0.0379). </div><div>In summary, miR-362-3p was identified to regulate hERG, and reduces proliferation of breast cancer cells through a mechanism that may be partially mediated by hERG inhibition. While miR-362-3p may have modest effects in cancer, in Aim 2 we demonstrated that it along with HF status accounts for a significant amount of variability in QTF prolongation following ibutilide administration. However, it is common for several miRNAs to regulate a single ion channel. Therefore, an HT-bioassay was developed to identify all miRNAs that potentially regulate KCNH2 during HF. In addition to miR-362-3p, thirty-one miRNAs were predicted to regulate KCNH2; one miRNA (miR-4665-5p) was significantly associated with QTF prolongation. The potential for miR-362-3p and HT-bioassay-identified miRNAs to reduce hERG-related current and influence susceptibility to drug-induced QT interval prolongation warrants further investigation. </div><div><br></div>

The liver is a multi-functional and highly regenerative organ. While resilient, the liver is susceptible to organ damage and failure. In both the acute and chronic settings liver disease has dire consequences for health. A common cause of liver damage is adverse reactions to drugs which can lead to drug induced liver injury (DILI). This creates major problems for patients, clinicians, the pharmaceutical industry and regulatory authorities. In the context of drug overdose or serious adverse reactions, liver failure can be acute and life threatening, and in some cases require orthotopic liver transplantation. While transplantation is highly successful, such an approach has limitations and justifies basic science attempts to develop better human models to study liver injury and to develop scalable intervention strategies. With this in mind, we have studied the importance of microRNAs (miRs) in regulating human drug metabolism in pluripotent stem cell – derived hepatocytes and their potential to reduce liver toxicity in response to toxic levels of paracetamol. miRs are small non-coding RNAs that are approximately 20 - 24 nucleotides long and their major function is to fine tune gene expression of their target genes. Recently, it has been demonstrated that microRNAs play a role in regulating the first phase of drug metabolism however the second phase of drug metabolism, drug conjugation, has not been studied in detail. Drug conjugation is a crucial stage in human drug metabolism, and any alterations in this process can lead to changes in compound pharmacology, including therapeutic dose and clearance from the body. To test the importance of miRs in regulating phase II drug metabolism we opted to study the metabolism of a common used analgesic, paracetamol. When taken in the appropriate amounts paracetamol is modified by sulfotransferases (SULTs) and UDP - glucuronosyltransferases (UGTs) and removed from the body without organ damage. However, when paracetamol is taken above the recommended dose it is metabolised by phase I enzymes to generate a toxic intermediate N-acetyl-p-benzoquinone imine (NAPQI), which if untreated can lead to massive hepatocyte cell death and liver failure, placing the patient in a life threatening situation. In order to promote non-toxic drug metabolism, in the context of drug overdose, we employed candidate miRs to regulate different parts of the paracetamol metabolism pathway. In summary, we have focused on studying human drug metabolism in the major metabolic cell type of the liver, the hepatocyte. We have identified a novel microRNA (called miR-324-5p) which regulates phase II drug metabolism and reduces cell cytotoxicity. Additionally, a supportive role of anti-microRNA- 324 in response to fulminant plasma collected from paracetamol overdose patients is also observed. The findings of this project are novel, provide proof of concept and exemplify the power of stem cell based models to identify new approaches to treating human liver damage.

Oligodendroglial tumours originate from oligodendrocytes usually arising in the white matter and could be classified into grade-II oligodendrogliomas (OD) and anaplastic oligodendrogliomas (AOD, grade-III) according to the 2016 World Health Organization (WHO) grading scheme. ODs1 could be diagnosed by pathological and immunohistochemical analyses, however recent evidence suggests that they could be better diagnosed on the basis of defined genetic entities, such as the combined loss of chromosome 1p and 19q arms and IDH mutation. 1p/19q co-deletion is molecular hallmark of ODs and is clinically associated with better prognosis, response to chemo/radio-therapy and overall survival. Typical oligodendroglial histological features are strongly associated with 1p/19q loss and IDH mutation, which is critically important as diagnostic point of view. The examining of exclusive molecular signatures and transcriptome expression profiles added to histological class could compliment the classification of OD subtypes. In this regard, microRNAs (miRNAs, miRs) profiles could serve classifier signatures for tumour subsets. MiRNAs are 22nt short non-coding RNAs which are expressed endogenously and regulate diverse cellular process through negative control on gene expression at the posttranscriptional level by direct or imperfect interaction with their target mRNAs. MiRNAs are involved in regulating human tumorigenesis acting as either tumour suppressors or oncogenes. During the passage of tumorigenesis miRNA expression level is significantly increased or decreased compared to corresponding normal tissue. The same is observed with their mRNAs. Therefore, transcriptome profiling of human tumours could identify signatures associated with progression, diagnosis, prognosis and response to therapy. However, until recently the information regarding the expression of miRNAs and mRNA in oligodendroglial tumours is scarce. In this study we performed miRNA and mRNA differential expression profiling between grade II and grade III ODs using microarray based expression profiling platforms (723 transcripts and 41,000 genes, respectively). 7 cases for OD grade-II, and 7 for AOD grade-III, and 15 non neoplastic white matter (nnWM) samples were used after microdissection with no previous history of treatment. We performed a systematic evaluation of miRNAs and mRNAs expressions and determined miRNAs and putative target genes that are differentially expressed in grade III AOD, but not in grade II OD and in non-neoplastic white matter (nnWM). 1 ODs when used with ,,s\" will represent both OD and AOD. 50 miRNAs were overexpressed and 43 were down regulated in AOD-III, whereas 7 miRNAs showed significant reduction in expressions in OD-II group. 3 miRNAs were commonly down regulated in comparisons of both groups. The hsa-miR-23a was strongly upregulated and hsamiR-27a was strongly downregulated in AOD-III. The functions of hsa-miR-23a and hsa-miR- 27a were tested in human adult fibroblasts for cell proliferation assay and apoptosis detection. Cells treated with pre-miR-23a and pre-miR-27a showed 20% reduction in cell proliferation as compared with controls. Further, the functional relevance of miRNAs to their target mRNAs was validated for each group, using real time qPCR. 10 key-miRNAs from AOD were subjected to validation by qPCR. We were able to confirm 7 miRNAs (p? 0.05). Among these, 5 miRs (miR- 193a-3p, miR-24, miR-27a, miR-30a-5p and miR-30c) showed reduced expression whose target genes (CCND1, HDAC2, PDGFA and RAB-26) were upregulated. Whereas, 2 miRNAs likewise miR-301b and miR-378 were overexpressed whose target genes BCL2, FGF2, CD44 and PPP4R4 confirmed by qPCR (p? 0.05). Bioinformatics based gene ontology (GO), and networking analysis revealed that differential expression and targets are attributed to differentiation of embryonic stem cells, cell adhesion, angiogenesis and neurogenesis, resistance to apoptosis, protein-protein interactions and cell proliferation. It was possible to identify and validate miRNAs and their mRNA-targets potentially involved in the progression of oligodendrogliomas particularly in grade III-AOD. Collectively, this analysis provides new insights to malignant progression of oligodendroglial tumours and could compliment WHO-2016 diagnosis scheme and may provide predictive outcome in patients as well as decision to therapy. / Oligodendrogliomas originários de oligodendrócitos que geralmente surgem na substância branca podendo ser classificados em grau oligodendroglioma (II-OD), e anaplastic oligodendrogliomas (grau III-AOD). Os ODs2 podem ser diagnosticados por análises patológicas e imuno-histoquímicas, porém evidências recentes sugerem que poderiam ser melhor diagnosticados com base em assinaturas moleculares, como a deleção combinada dos cromossomas 1p e 19q - marcadores moleculares dos OD associados clinicamente a um melhor prognóstico, resposta à terapia e melhor sobrevida. As características histológicas típicas dos oligodendrogliomas também estão fortemente associadas à deleção de 1p/19q, que é criticamente importante como ponto de vista diagnóstico. Assim, os subtipos de gliomas podem ser fortemente diferenciados não somente em relação ao seu perfil histológico mas também com base em seu perfil de expressão genica e suas assinaturas moleculares exclusivas. Os microRNAs (miRNAs, miRs) emergiram como assinaturas moleculares para os diferentes graus. Os miRNAs são RNAs não codificantes, contendo em torno de 22 nucleótidos. São expressos endogenamente e regulam diversos processos celulares através do controle negativo da expressão gênica em nivel pós-transcricional e por interacção directa ou imperfeita com o RNAm-alvo. Os miRNAs estão envolvidos na regulação da tumorigenese humana atuando como supressores de tumour ou oncogenes. Durante o processo da tumorigenese o nível de expressão dos miRNAs é aumentado ou diminuído significativamente em comparação com tecido normal correspondente. O perfil de expressão de miRNA de tumores humanos poderia identificar assinaturas associadas com progressão, diagnóstico, prognóstico e resposta à terapia. Contudo, até recentemente a informação sobre a expressão de miRNAs em oligodendrogliomas é escassa. Neste estudo, avaliamos o perfil de expressão diferencial de miRNA e RNAm em ODs graus II e III usando plataformas de perfis de expressão baseadas em microarray (723 transcritos e 41.000 genes, respectivamente). Foram utilizados 14 casos de ODs microdissecados, sendo 7 OD grau II, e 7 AOD grau III (anaplasicos) sem histórico prévio de tratamento, além de 15 amostras de substancia branca não neoplásica (nnSB). Por meio de avaliações sistemáticas foram determinados miRNAs e mRNAs expressos em AOD grau III, mas não em OD grau II e em substancias brancas não neoplásicas (nnSB). 2 ODs when used with ,,s\" will represent both OD and AOD. Assim, foram encontrados 50 miRNAs com alta expressão e 43 miRNAs com baixa expressão em AOD-III, enquanto que 7 miRNAs apresentaram expressões reduzidas no grupo OD-II. Na comparação entre os dois grupos, 3 miRNAs apresentaram baixa expressão. A hsa-miR-23a mostrou alta expressão e a hsa-miR-27a apresentou uma diminuição de expressão importante em AOD III. A atividade dos hsa-miR-23a e hsa-miR-27a foram testadas em células de fibroblastos adultos humanos usando ensaios de proliferação celular e detecção de apoptose. As células tratadas com pre-miR-23a e pre-miR-27a mostraram 20% redução de proliferação celular em comparação com os controles. Para cada grupo, a relevância funcional dos miRNAs e seus mRNAs alvos foi validada utilizando qPCR. Dos 10 miRNAs submetidos a validação em grau III, foi possivel confirmar 7 miRNA(p<0,05). Entre esses, 5 miRs (miR-193a-3p, miR-24, miR- 27a, miR-30a-5p e miR-30c) mostraram expressão reduzida, cujos genes alvos (CCND1, HDAC2, PDGFA e RAB-26) apresentavam alta expressão. Enquanto que, 2 miRNAs como miR-301b e miR-378 apresentaram alta expressão cujos genes alvo BCL2, FGF2, CD44 e PPP4R4 foram confirmados por qPCR (p<0,05). Ferramentas de bioinformática (Gene Ontology) e a análises em rede revelaram que a expressão diferencial e os alvos são atribuídos à diferenciação de células-tronco embrionárias, adesão de celular, angiogênese e neurogênese, resistência à apoptose, interações proteína-proteína e proliferação celular. Foi possível identificar e validar miRNAs e RNAm-alvos potencialmente envolvidos na progressão de oligodendrogliomas. Coletivamente, esta análise fornece novos achados relacionados a progressão maligna de tumores oligodendrogliais e poderia facilitar o diagnóstico preciso e mais restritivo, o desfecho preditivo em pacientes, bem como auxiliar na decisão da terapia.

MicroRNAs play an important role in biological regulation. Recently miR-34a has been reported to regulate tumour cell cycle progression and apoptosis. However, the functional role of miR-34a in smooth muscle cell (SMC) differentiation from stem cells is yet unclear. Main objectives of this PhD project are to determine the functional role of miR-34a and its target genes in SMC differentiation and underlying mechanisms. Mouse embryonic stem (ES) cells were seeded on collagen coated flasks in differentiation medium to allow SMC differentiation. Upon analysis, miR-34a was significantly up-regulated during SMC differentiation. Results demonstrated that overexpression of miR-34a significantly promoted SMC-specific gene expression, while knockdown of miR-34a inhibited expression of SMC specific gene. Enforced expression and knockdown of miR-34a in differentiating ES cells up-regulated and down-regulated, respectively, several SMC transcription factors in a similar manner. It was also found that miR-34a overexpression in stem cells promoted SMC differentiation in vivo. Furthermore, deacetylase sirtuin 1 (Sirt1) was identified as one of the top targets of miR-34a. Surprisingly, Sirt1 was demonstrated to be positively regulated by miR-34a during SMC differentiation in a cellular context and RNA sequence dependent manner. VIII Mechanistically, the data suggested that miR-34a promoted differentiating stem cells arrest at G0/G1 phase, and a significant decreased incorporation of miR-34a and SirT1 RNA into Ago2-RISC complex was observed upon SMC differentiation. The results demonstrated that Sirt1 acted as a transcriptional activator in the regulation of SMC gene during ES cell differentiation. Finally, H3K9 tri-methylation around the promoter regions of the SMαA and SM22α genes was also found to be significantly inhibited by SirT1 overexpression. These findings suggest that miR-34a plays an important role in SMC differentiation from ES cells. Meanwhile, Sirt1 can be regulated by miR-34a through an unexpected pathway and it was identified as a functional modulating target in miR-34a mediated SMC differentiation.

The MEF2 transcription factor is a central regulator of skeletal and cardiac muscle development. Recently, we showed that MEF2A regulates skeletal muscle regeneration through direct regulation of the Gtl2-Dio3 microRNA mega-cluster. In addition to their expression in skeletal muscle, temporal expression analysis of selected Gtl2-Dio3 microRNAs revealed high enrichment in cardiac muscle. Therefore, I investigated the role of selected microRNAs from the Gtl2-Dio3 noncoding RNA locus in the heart. First, I found that Gtl2-Dio3 microRNAs are expressed at higher levels in perinatal hearts compared to adult, suggesting they function in cardiac maturation shortly after birth. I also demonstrated that these microRNAs are dependent on MEF2A in the perinatal heart and in neonatal cardiomyocytes. To determine the specific role in cardiac muscle, I overexpressed selected microRNA mimics in neonatal rat ventricular myocytes (NRVMs). My results showed that miR-410 and miR-495 stimulate cell cycle re-entry and proliferation of terminally differentiated NRVMs. Subsequent target prediction analyses revealed a number of candidate target genes known to function in the cell cycle and/or in cardiac muscle. One of these was Cited2, a cofactor required for proper cardiac development. Subsequently, I showed that Cited2 is a direct target of these miRNAs and that siRNA knockdown of Cited2 in NRVMs resulted in robust cardiomyocyte proliferation. This phenotype was associated with reduced expression of Cdkn1c/p57/Kip2, a cell cycle inhibitor, and increased expression of Vegfa, a growth factor with proliferation-promoting effects. Given the exciting possibility of manipulating the expression of these microRNAs to repair the damaged heart by stimulating cardiomyocyte proliferation, I then investigated whether they were regulated in cardiac disease and function in pathological signaling. Toward this end, I examined expression of miR-410, miR-495, miR-433, as well as the Gtl2 lncRNA in various cardiomyopathies. Interestingly, the microRNAs and lncRNA were dynamically regulated in mouse models of cardiac disease including myocardial infarction and chronic angiotensin II stimulation. Furthermore, I showed for the first time that the Gtl2 lncRNA and miRNAs are differentially regulated in myocardial infarction, indicating that the complex regulation of the Gtl2-Dio3 noncoding RNA locus may be important for response to cardiac injury. Lastly, I showed that inhibiting select Gtl2-Dio3 microRNAs in pathological signaling attenuated cardiomyocyte hypertrophy in vitro. Therefore, differential targeting of the Gtl2-Dio3 noncoding RNAs could provide new therapeutic strategies to control the response of the heart to cardiac diseases with diverse etiologies.

Germ cell tumours (GCTs) are clinically and pathologically heterogeneous neoplasms that arise at gonadal (testicular/ovarian) and extra-gonadal sites. The chemotherapy burden for patients with malignant germ cell tumours (mGCTs) that require treatment results in substantial longterm side-effects, and, furthermore, poor-risk patients have < 50% survival. Consequently, identifying common molecular changes and novel therapeutic targets in mGCTs is of major clinical importance. MicroRNAs are short, non-protein coding RNAs that regulate gene expression. We previously showed that miR-99a-5p/-100-5p and miR-125b-5p are among the most frequently underexpressed microRNAs in mGCTs, regardless of anatomical site, histological type or patient age. The present study investigates the upstream causes and downstream consequences of such under-expression. The mature form of miR-125b-5p is the product of two genomic loci, which form a cluster with either miR-99a-5p (on chromosome 21q) or miR-100-5p (on chromosome 11q). MiR-99a-5p/- 100-5p share identical 'seed' regions (at nucleotide positions 2-7), which determine their mRNA targets. Cross-reactivity experiment revealed that both miR-99a-5p and miR-100-5p probes were highly cross-reactive to each other's target (from 91% to 95%), indicating functional overlap. Linear regression analysis of qRT-PCR data reveals a strong positive correlation between miR-99a-5p/-100-5p and miR-125b-5p levels (R2 =0.989) in mGCTs, strongly suggesting co-regulation. Primary microRNA transcripts (pri-miR-99a/-100 and pri-miR-125b), and other genes that colocalise to these miRNA clusters (e.g. BLID on chromosome 11), were quantified by RT-qPCR in four representative cell lines - TCam2, 1411H, 2102Ep, and GCT44 - which were derived from a range of common histological types of mGCTs. A significant down-regulation (p < 0.0001) of all primary transcripts was observed, suggesting transcriptional repression of the entire cluster regions. Treatment of the cell lines with 5'-azacytidine resulted in significant upregulation of all three miRNAs (p < 0.002), as well as BLID (p < 0.02). The methylation status of potential CpG islands at the region of interest on chromosome 11 and chromosome 21 was therefore investigated by Pyrosequencing. Significant hyper methylation was found in 2102Ep, 1411H and GCT44 cell lines, suggesting that the miR-99a-5p/-100-5p and miR-125b-5p clusters are likely transcriptionally silenced by DNA methylation. To assess the functional relevance of these microRNAs in GCT progression, co-transfection of microRNA mimics (8.3 nM miR-99a-5p/-100-5p + 8.3 nM miR-125b-5p) was performed. A significant decrease in cell growth was seen in 1411H (p < 0.01) and TCam2 (p < 0.03) cells. To identify the mimics' downstream mRNA targets, HumanHT-12 v4 Expression Bead Chip (Illumina) mRNA arrays were used and data analysed using Sylamer. This analysis showed that mimic-treated cells were enriched in downregulated genes involved in pro-proliferative mechanisms. Among those, further functional characterisation focussed in particular on TRIM71, FGFR3, E2F7 and LIN28A. Moreover, restoring miR-99a-5p/-100-5p and miR-125b-5p in TCam2 cells also resulted in G0-G1 accumulation, consistent with a cell cycle effect. These data support a functionally important role for miR99a-5p/-100-5p and miR-125b-5p in GCT progression. They also raise the possibility of a therapeutic replenishment approach for treating these, and potentially other, tumours.

Toxoplasma gondii is an obligate intracellular parasite, that is able to infect any nucleated cell. An important global pathogen, T. gondii can cycle between primary and secondary hosts, thus enabling widespread penetrance. Within its intracellular niche – a membrane-bound parasitophorous vacuole – T. gondii is nevertheless able to subvert a variety of host cell processes to allow its continued survival and replication. This includes modulation of host signalling processes as well as the scavenging of nutrient macromolecules. In recent years, microRNAs have emerged as important regulators of cellular processes including inflammation, tumorigenesis and metabolism, as well as development. It has become increasingly clear that this species of non-coding RNA is of great importance in ‘fine tuning’ many cellular responses. I hypothesise in this work that host cell miRNAs may be yet another means by which T. gondii manipulates its host upon infection. Using high-throughput-sequencing, I examine host cell transcriptional responses to infection both at the mRNA and microRNA level, using two strains of T. gondii at a variety of Multiplicities of Infection over a time course of 43 hours. Through these transcriptional analyses I identify a number of dysregulated pathways common in tumorigenesis, and contemplate the hypothesis that T. gondii may be behaving as an ‘intracellular tumour’, subverting host cell metabolic processes to mimic a long-known feature of cancer metabolism – that of aerobic glycolysis (the Warburg effect) – in order to satisfy its own energetic and metabolic needs.

Submitted by CARINA DE FÁTIMA DE SIBIA null (carinasibia@gmail.com) on 2017-02-21T19:28:25Z No. of bitstreams: 1 tese final 21.2.pdf: 1461578 bytes, checksum: aaee8aaa84b0ad8485b183d6dc28a095 (MD5) / Rejected by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br), reason: O arquivo submetido está na orientação paisagem, o arquivo deve estar na orientação retrato on 2017-02-24T19:02:56Z (GMT) / Submitted by CARINA DE FÁTIMA DE SIBIA null (carinasibia@gmail.com) on 2017-02-24T22:08:47Z No. of bitstreams: 1 tese .pdf: 1294801 bytes, checksum: dd9a234277b605736e3567a3692c2d48 (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-03-06T16:57:54Z (GMT) No. of bitstreams: 1 sibia_cf_me_bot.pdf: 1294801 bytes, checksum: dd9a234277b605736e3567a3692c2d48 (MD5) / Made available in DSpace on 2017-03-06T16:57:54Z (GMT). No. of bitstreams: 1 sibia_cf_me_bot.pdf: 1294801 bytes, checksum: dd9a234277b605736e3567a3692c2d48 (MD5) Previous issue date: 2017-01-31 / Introdução: A doença de Crohn (DC) e a retocolite ulcerativa (RCU) são as duas principais doenças que compõem a doença inflamatória intestinal (DII). Estudos indicam que vários genes estão diferencialmente expressos em DC. vs. RCU. Entretanto, os mecanismos moleculares de desenvolvimento e progressão das diferentes formas da DII ainda não foram elucidados. Considerando que os microRNAs (miRNAs) são potentes reguladores da expressão gênica e têm papel importante em várias doenças humanas, estes podem constituir biomarcadores com potencial diagnóstico, prognóstico e terapêutico em DII. Objetivos: Identificar miRNAs desregulados em DII, distinguindo DC e RCU; identificar genes-alvo dos miRNAs alterados e redes de interação entre miRNAs e genes-alvo em DII. Materiais e Métodos: Foi utilizada estratégia de meta-análise para identificação de dados de expressão de miRNAs em DII. Após aplicação dos critérios de inclusão e exclusão, foram selecionados 10 estudos para extração dos dados. Desses estudos, foram identificados miRNAs significativamente desregulados (nível de alteração ou FC>=2 e p<0,05) e coletadas informações sobre o tipo e o número de amostras analisadas (soro, plasma ou tecido) de pacientes com DC ou RCU, plataformas utilizadas para análise de expressão de miRNAs e validação dos dados, entre outras. A seguir, foram aplicadas as ferramentas de bioinformática mirwalk 2.0 para predição de genes-alvo regulados pelos miRNAs e STRING e BiNGO para identificação de redes de interação entre miRNAs e genes-alvo e funções biológicas, respectivamente. Resultados: Entre os miRNAs com expressão aumentada, foram identificados 17 em DC e 62 em RCU. Entre os miRNAs com expressão diminuída, foram identificados 18 em DC e 31 em RCU. Os miRNAs que mostraram o maior número de interações com genes-alvo na DC foram: let-7a-5p, let-7b-5p, miR-199a-5p, miR-150-5p, miR-362-3p e miR-224-5p. Em RCU, os miRNAs desregulados e com maior número de interações foram miR-155-5p, miR-24-5p, miR-335-5p e miR-16-5p. Conclusões e Perspectivas Futuras: Foram identificadas redes de interação entre miRNAs e genes-alvo associados a processos biológicos de inflamação e resposta imune. Os miRNAs identificados modulam vias moleculares potencialmente envolvidas na patogênese da DII. Estudos como esse podem contribuir para a melhoria do diagnóstico e no desenvolvimento de tratamentos direcionados e mais precisos para pacientes com DC e RCU.

Em bovinos, o desenvolvimento embrionário pré implantacional depende das funções do endométrio bovino que tem suas funções mediadas por uma complexa interação da ação e dos efeitos dos hormônios esteroides ovarianos E2 e P4. Estes hormônios regulam a expressão gênica e controlam o ambiente uterino modulando, entre outros, a expressão de microRNAs e a rede de citocinas relacionadas ao sistema imune. Os objetivos do presente trabalho foram abordados em dois capítulos, sendo (I) comparar os efeitos dos distintos ambientes endócrinos peri-ovulatórios sobre a expressão de microRNAs (II) e na modulação do sistema IL1/TLR no endométrio bovino nos dias 4 e 7 após a indução da ovulação. Para isso, controlou-se farmacologicamente o crescimento do folículo objetivando induzir a ovulação de folículos de maior diâmetro (grupo folículo grande-CL grande, FG-CLG) ou de menor diâmetro (grupo folículo pequeno-CL Pequeno, FP-CLP). Vinte e duas vacas multíparas nelore, foram pré-sincronizadas, metade destes animais foram destinados para o grupo FG-CLG e receberam uma dose de prostaglandina F2&#945; (PGF) e um dispositivo de progesterona, juntamente com benzoato de estradiol no D10. No momento da retirada dos dispositivos de progesterona (entre D1,75 e D2,5) todos os animas receberam uma dose de PGF. A ovulação foi induzida com acetato de buserelina (D0). O que diferiu entre os tratamentos foi que os animais do grupo FP-CLP não receberam uma dose de PGF no D10 e o momento da retirada dos dispositivos foi entre D1,25 e o D1,5. No capítulo I, o a expressão de microRNAs foi determinada por qPCR nos dias 4 e 7. Dos 90 microRNAs testados, 21 apresentaram se up-regulated e dois down-regulated no grupo FG-CLG (P<0.1) no D4. No D7, quatro microRNAs foram diferentemente expressos, sendo um up-regulated e três down-regulated no grupo FG-CLG (P<0.1) no D7. Para os microRNAs diferentemente expressos determinou-se mRNA-alvos preditos. Uma análise de ontologia demonstrou que os mRNAs-alvos apresentaram enriquecimento funcional na via dos receptores de hormônios esteroides, entre outras. No capítulo II, o sistema IL1/TLR foi avaliado quanto a abundância de transcriptos envolvidos neste sistema, do microRNA bta-mir-155 e das proteínas IL1&#946; e IL1R1. A abundância relativa de mRNA apresentou diferença (P<0.1) na abundância dos mRNAs de IL1R1, TAB1 e FOXP3, das proteínas IL1&#946; e IL1R1, sendo essas moléculas up-regulated no grupo FG-CLG. O microRNA bta-mir-155 foi down-regulated no grupo FG-CLG (P<0.1). Diante disto, pode-se concluir que o ambiente endócrino peri-ovulatório determina o perfil de expressão de microRNAs e modula o sistema IL1/TLR no endométrio bovino / In cattle, the pre implantation embryo development depends on the functions of the bovine endometrium that has its functions mediated by a complex interaction of action and the effects of ovarian steroid hormones E2 and P4. These hormones regulate gene expression and control the modulating uterine environment among others, the expression of microRNAs and the network of cytokines related to the immune system. The objectives of this study were discussed in two chapters, (I) to compare the effects of different peri-ovulatory endocrine environment on the expression of microRNAs (II) and modulation of the IL-1 system / TLR in bovine endometrium on days 4 and 7 after induction of ovulation. For this, it was controlled pharmacologically follicle growth aiming to induce ovulation of follicles larger diameter (great grand-CL follicle group, FG-CLG) or smaller in diameter (small-CL Small follicle group, FP-PLC). Twenty two nelore multiparous cows were pre-sync, half of these animals were used for the FG-NCG group and received a dose of F2á prostaglandin (PGF) and progesterone device along with oestradiol benzoate in D-10. Upon withdrawal of progesterone devices (between 1.75 and D-D-2,5) all animas received a dose of PGF. Ovulation was induced with buserelin acetate (D0). What differed between treatments was that animals FP-CLP group did not receive a dose of PGF in the D-10 and the time of removal of the devices was between D-1,25 and D-1.5. In Chapter I, the expression of microRNAs was determined by qPCR on 4 and 7. Of the 90 microRNAs tested, 21 showed was up-regulated and down-regulated in two FG-CLG group (P <0.1) in the D4. In D7 four microRNAs were differently expressed, one up-regulated and down-regulated in three FG-CLG group (P <0.1) at D7. For differently expressed microRNAs was determined predicted mRNA-target. An ontology analysis showed that the mRNA-targets had functional enrichment in via the steroid hormone receptors, among others. In Chapter II, the IL-1 / TLR system was evaluated as the abundance of transcripts involved in this system, the bta-mir-155 microRNA and IL1&#946; and IL1R1 proteins. The relative abundance of mRNA was different (P <0.1) in the abundance of mRNAs IL1R1, TAB1 and FOXP3, the IL1&#946; and IL1R1 proteins, and these up-regulated molecules in the FG-CLG group. The bta-mir-155 microRNA was down-regulated in the FG-CLG group (P <0.1). Given this, we can conclude that the peri-ovulatory endocrine milieu determines the profile of microRNA expression and modulates the IL1 / TLR system in bovine endometrium