<p>Glioblastoma (GBM) represents the most common and lethal brain tumor in adults, with glioma initiating cells (GICs) implicated to play a critical role in its progression and recurrence. However, the molecular mechanisms underlying the distinct function of GICs and non-GICs remain largely unknown. Elucidating distinct molecular features of GICs will pave the foundation for GIC directed therapies for GBM treatment. </p><p>We first demonstrated that GICs preferentially express two interleukin 6 (IL6) receptors: IL6 receptor alpha (IL6Ra) and glycoprotein 130 (gp130). Targeting IL6Ra; or IL6 ligand expression in GICs using short hairpin RNAs (shRNAs) significantly reduces growth and neurosphere formation capacity while increasing apoptosis. Block IL6 signaling in GICs attenuates Stat3 activation, and small molecule inhibitors of STAT3 potently induce GIC apoptosis. Targeting IL6Ra; or IL6 expression in GICs increases the survival of mice bearing intracranial human glioma xenografts. The promising application of anti-IL6 therapies is demonstrated by decreased subcutaneous tumor growth of human GIC-derived xenografts treated with IL6 antibody. Together, our data indicate that IL6 signaling contributes to glioma malignancy through the promotion of GIC growth and survival, and that targeting IL6 may offer benefit for glioma patients.</p><p>MicroRNAs (miRNAs) are a class of non-coding small RNA molecules which negatively regulate gene expression and are deregulated in many types of cancer. Through a candidate-based screen, we identified microRNA-33a as a master determinant whose expression controls the functional differences between GIC and non-GICs. Antagonizing miR-33a function in GICs led to reduced self-renewal and tumor progression in immune-compromised mice, whereas overexpression of miR-33a in non-GICs rendered them to display features associated with GICs. Mechanistically, miR-33a acts to confer the biological property of GICs via enhancing the activities of cAMP/PKA pathway and Notch signaling by targeting negative regulators of these two pathways. Together these findings reveal a miR-33a-centered signaling network that dictates the identity/activity of GICs and consequently serves as a therapeutic target for the treatment of GBM.</p><p>In summary, this doctoral thesis reveals two novel molecular events that characterize the distinct feature of GICs and develops preclinical strategies for the therapeutic application of GBM.</p> / Dissertation

Abstract Ascoviruses (AVs) are members of the family Ascoviridae that are transmitted by female endoparasitic wasps and cause lethal infection in lepidopteran insects. AVs possess large double stranded DNA genomes ranging from 116-186 kbp. Recently, genomes of four AV species have been completely sequenced and have revealed important genes potentially needed for virus DNA replication and infection. Phylogenetic analyses of several of these genes indicate that AVs are closely related to iridoviruses and likely evolved from them. Two unique features, mode of transmission and cytopathology which involves cleavage of cells into virus-containing vesicles, make AVs different from other insect pathogenic viruses. During this decade, tremendous advancements in the study of RNA silencing mechanisms have openned a new dimension in virology. It is now evident that viruses reshape the cellular environment by reprogramming host RNA silencing machinery. The process of RNA silencing involves small non-coding RNAs, which with the help of nuclease-containing regulatory proteins bind to complementary messenger RNA (mRNA) targets, resulting in inhibition of gene expression. This sophisticated style of gene regulation has attained a fundamental status in living organisms, since RNA silencing has been revealed to be ubiquitous from viruses to prokaryotes to eukaryotes. Two main categories of small RNAs, short interfering RNA (siRNA) and microRNA (miRNA), have been defined as major players in RNA silencing. Interestingly, viral genomes like that of their hosts, encode miRNAs that can be used during virus invasion to manipulate host genes as well as miRNA biogenesis. Here, we report on the identification of the first insect virus miRNA (HvAVmiR- 1) derived from the major capsid protein (MCP) gene of Heliothis virescens ascovirus 7 (HvAV3e). HvAV-miR-1 expression was found to be strictly regulated and specifically detected from 96 h post-infection. HvAV-miR-1 expression coincides with a marked reduction of the expression of HvAV3e DNA polymerase I, which is a predicted target. Ectopic expression of the full-length and truncated versions of MCP retaining the miRNA sequence significantly reduced DNA polymerase I transcript levels and inhibited viral replication. Our results indicate that HvAV-miR-1 directs degradation of DNA polymerase I transcripts and regulates replication of HvAV3e. Further, we investigated changes in the expression levels of host miRNAs upon HvAV3e infection in an insect cell line derived from Helicoverpa zea fat body and investigated the role of a host miRNA, Hz-miR24, in the hostvirus system. It was found that Hz-miR24 is differentially expressed following virus infection, with an increase in its expression levels late in infection. Functional analyses demonstrated that Hz-miR24 targets viral DNA-dependent RNA polymerase and its β subunit mRNAs. This was confirmed using ectopic expression of Hz-miR24 and a green fluorescent protein-based reporter system. Expression of the target gene was substantially enhanced in cells transfected with a synthesized inhibitor of Hz-miR24. These findings suggest that ascoviruses encode their own miRNA(s) and concurrently manipulate host miRNAs that in turn regulate the expression of their genes at specific time points after infection. In connection to RNA silencing, we characterized a ribonuclease III (RNase III) protein encoded by HvAV3e. We found that RNase III protein was functional in vivo as well as in vitro and catalyzed long and short double stranded RNAs. Expression analyses during virus infection revealed autoregulation of this protein by degradation of its RNA transcripts. Moreover, RNase III protein was found to be involved in suppression of RNA silencing and essential for virus DNA replication and infection. Finally, we studied another ascoviral 8 protein, a putative inhibitor of apoptosis (IAP), which was found to be essential for virus DNA replication and pathology. Further, despite inhibition of apoptosis by HvAV3e, the IAP-like protein was found dispensable for the inhibition of replication. In conclusion, for successful invasion and attenuation of host antiviral responses, ascoviruses seem to utilize viral encoded proteins as well as miRNAs. Since the genomes of these viruses have only recently been sequenced, the role of many of the encoded genes essential for pathogenesis and manipulation of antiviral defence mechanisms remains to be eluciated.

Abstract Ascoviruses (AVs) are members of the family Ascoviridae that are transmitted by female endoparasitic wasps and cause lethal infection in lepidopteran insects. AVs possess large double stranded DNA genomes ranging from 116-186 kbp. Recently, genomes of four AV species have been completely sequenced and have revealed important genes potentially needed for virus DNA replication and infection. Phylogenetic analyses of several of these genes indicate that AVs are closely related to iridoviruses and likely evolved from them. Two unique features, mode of transmission and cytopathology which involves cleavage of cells into virus-containing vesicles, make AVs different from other insect pathogenic viruses. During this decade, tremendous advancements in the study of RNA silencing mechanisms have openned a new dimension in virology. It is now evident that viruses reshape the cellular environment by reprogramming host RNA silencing machinery. The process of RNA silencing involves small non-coding RNAs, which with the help of nuclease-containing regulatory proteins bind to complementary messenger RNA (mRNA) targets, resulting in inhibition of gene expression. This sophisticated style of gene regulation has attained a fundamental status in living organisms, since RNA silencing has been revealed to be ubiquitous from viruses to prokaryotes to eukaryotes. Two main categories of small RNAs, short interfering RNA (siRNA) and microRNA (miRNA), have been defined as major players in RNA silencing. Interestingly, viral genomes like that of their hosts, encode miRNAs that can be used during virus invasion to manipulate host genes as well as miRNA biogenesis. Here, we report on the identification of the first insect virus miRNA (HvAVmiR- 1) derived from the major capsid protein (MCP) gene of Heliothis virescens ascovirus 7 (HvAV3e). HvAV-miR-1 expression was found to be strictly regulated and specifically detected from 96 h post-infection. HvAV-miR-1 expression coincides with a marked reduction of the expression of HvAV3e DNA polymerase I, which is a predicted target. Ectopic expression of the full-length and truncated versions of MCP retaining the miRNA sequence significantly reduced DNA polymerase I transcript levels and inhibited viral replication. Our results indicate that HvAV-miR-1 directs degradation of DNA polymerase I transcripts and regulates replication of HvAV3e. Further, we investigated changes in the expression levels of host miRNAs upon HvAV3e infection in an insect cell line derived from Helicoverpa zea fat body and investigated the role of a host miRNA, Hz-miR24, in the hostvirus system. It was found that Hz-miR24 is differentially expressed following virus infection, with an increase in its expression levels late in infection. Functional analyses demonstrated that Hz-miR24 targets viral DNA-dependent RNA polymerase and its β subunit mRNAs. This was confirmed using ectopic expression of Hz-miR24 and a green fluorescent protein-based reporter system. Expression of the target gene was substantially enhanced in cells transfected with a synthesized inhibitor of Hz-miR24. These findings suggest that ascoviruses encode their own miRNA(s) and concurrently manipulate host miRNAs that in turn regulate the expression of their genes at specific time points after infection. In connection to RNA silencing, we characterized a ribonuclease III (RNase III) protein encoded by HvAV3e. We found that RNase III protein was functional in vivo as well as in vitro and catalyzed long and short double stranded RNAs. Expression analyses during virus infection revealed autoregulation of this protein by degradation of its RNA transcripts. Moreover, RNase III protein was found to be involved in suppression of RNA silencing and essential for virus DNA replication and infection. Finally, we studied another ascoviral 8 protein, a putative inhibitor of apoptosis (IAP), which was found to be essential for virus DNA replication and pathology. Further, despite inhibition of apoptosis by HvAV3e, the IAP-like protein was found dispensable for the inhibition of replication. In conclusion, for successful invasion and attenuation of host antiviral responses, ascoviruses seem to utilize viral encoded proteins as well as miRNAs. Since the genomes of these viruses have only recently been sequenced, the role of many of the encoded genes essential for pathogenesis and manipulation of antiviral defence mechanisms remains to be eluciated.

<p>MicroRNAs (miRNAs) are a class of small non-coding RNAs that control gene expression by targeting mRNAs and triggering either translation repression or RNA degradation. Several groups pointed out that miRNAs play a major role in several diseases, including cancer. This is assumed since the expression level of several miRNAs differs between normal and cancerous cells. Further, it has been shown that miRNAs are involved in cell proliferation and cell death.</p><p>Because of this role it is suspected that miRNAs could serve as biomarkers to improve tumor classification, therapy selection, or prediction of survival. In this context, it is questioned, among other things, whether miRNA deregulations in cancer cells occur according to some pattern or in a rather random order. With this work we contribute to answering this question by adapting two approaches (Beerenwinkel et al. (J Comput Biol, 2005) and Höglund et al. (Gene Chromosome Canc, 2001)), developed to derive graph models of oncogenesis for chromosomal imbalances, to miRNA expression data and applying them to a breast cancer data set. Further, we evaluated the results by comparing them to results derived from randomly altered versions of the used data set.</p><p>We could show that miRNA deregulations most likely follow a rough temporal order, i.e. some deregulations occur early and some occur late in cancer progression. Thus, it seems to be possible that the expression level of some miRNAs can be used as indicator for the stage of a tumor. Further, our results suggest that the over expression of mir-21 as well as mir-102 are initial events in breast cancer oncogenesis.</p><p>Additionally, we identified a set of miRNAs showing a cluster-like behavior, i.e. their deregulations often occur together in a tumor, but other deregulations are less frequently present. These miRNAs are let-7d, mir-10b, mir-125a, mir-125b, mir-145, mir-206, and mir-210.</p><p>Further, we could confirm the strong relationship between the expression of mir-125a and mir-125b.</p>

Le Gallid Herpesvirus 2 (GaHV-2) est un herpesvirus responsable de lymphomes T chez le poulet qui encode 25 miARN matures regroupés en deux clusters localisés au sein des régions TRL/IRL et TR/IR. Mes travaux ont consisté en l’étude de la régulation transcriptionnelle du cluster mdvl-miR-M8-M10 situé au sein de la région IR5/TR. Le promoteur est constitué d’au moins 2 séquences répétées de 60 pb contenant des éléments de réponse à la protéine p53. Nous avons montré que cette protéine classiquement suppresseur de tumeur était détournée de sa fonction par le virus au profit de l’expression du cluster de miR viraux. D’autre part, le promoteur de l’oncomiR-21 cellulaire, surexprimé au cours de la lymphomagenèse induite par GaHV-2 et localisé au niveau d’une région hyper conservée chez les vertébrés est piloté en partie par les protéines de la famille AP-1. Nous avons montré que l’oncoprotéine virale Meq surexprimée au cours de l’infection transactivait le promoteur de miR-21. Enfin, l’étude des cibles potentielles virale ou cellulaire du miR-21 semble indiquer que ce dernier pourrait être impliqué dans les mécanismes de latence virale et de lymphomagenèse / Gallid herpes virus 2 (GaHV-2) is an alphaherpesvirus involved in lymphomas on chickens that encodes 25 matures miRNA grouped in 2 clusters localized on IRL and TRL regions. In the first hand, I studied the transcriptional regulation of the mdvl-miR-M8-M10 cluster localized on IRS/TRS region. A promoter constituted of at last 2 repeats of 60 bp harbouring p53 responsive element was identified. We showed that tumour suppressive protein p53 was diverted from its function to permit viral miRNA expression. On the second hand, the promoter of the cellular oncomiR-21, over expressed during GaHV-2 lymphomagenesis localized in a region highly conserved on vertebrate and was piloted by AP-1 proteins. We have shown that viral oncoprotein Meq overexpressed during infection transactivated gga-miR-21 promoter. At last, study ofpotential viral and cellular targets for gga-mir-21 seemed to indicate that gga-miR-21could be involved in viral latency establishment and lymphomageneSis.

Le Gallid Herpesvirus 2 (GaHV-2) est un herpesvirus responsable de lymphomes T chez le poulet. Son génome code pour 25 miARN matures regroupés en 2 clusters localisés au sein des régions répétées TRL/IRL etIRS/TRS. Mon travail a tout d’abord consisté en l’étude de la fonctionnalité des deux brins de mdv1-pré-miRM4sur deux cibles virales UL-28 et UL32. Le brin mdv1-miR-M4-5P ayant été identifié comme orthologue dumiARN cellulaire miR-155, leurs impacts ont été comparés sur six cibles cellulaires et la cible virale UL-28.Les différents miARN de GaHV-2 présentant des taux d’expression variables, nous avons identifié, dans larégion TRL/IRL, des ARNm responsables de leur transcription à partir d’exon ou d’intron. De plus, nous avonsidentifié un promoteur plutôt spécifique de la latence et responsable de la transcription de l’ensemble desmiARN de l’IRL/TRL, de l’oncogène meq et du transcrit Meq/vIL-8. / Gallid Herpesvirus 2 (GaHV-2) is a herpesvirus inducing T-lymphoma in chickens. Its genome encodes 25mature miRNAs splitted in two clusters localized in IRL/TRL and IRS/TRS repeated regions. In this work, wefirst analyzed the functionality of the two strands of mdv1-pre-miR-M4 on two viral targets named UL-28 andUL-32. As one strand of this miRNA was identified as an ortholog of cellular miRNA-155, their effects wereassessed on six cellular targets and on the UL-28 viral target. As a differential expression of miRNAs wasobserved during GaHV-2 infection, we found numerous IRL/TRL transcripts responsible for the intronic orexonic transcription of viral miRNAs. Moreover, we identified a latency promoter controlling at the same timetranscription of all IRL/TRL miRNAs, the oncogenic meq gene and the Meq/v-IL8 transcript.

RNA silencing is a major regulator of gene expression in plants, controlling from development to transposable element silencing and stress responses. As part of the silencing machinery, micro (mi)RNAs orchestrate silencing of their targets, either directly or through cascades of secondary small interfering (si)RNAs. To investigate the role of RNA silencing in plant immunity, I chose to focus on the miR482/2118 family, because of its diversity and presence in many plant species since the appearance of seed plants, with most genomes containing several copies, and because its members target sequences conserved in a family of disease resistance genes known Nucleotide biding site leucine-rich repeat (NLR) genes. In this dissertation, I wanted to address the extent to which the miRNA family and its derived phasiRNAs regulate expression of defence genes as well as contribute to quantitative resistance in crops. I explore the structural differences of miR482/2118 members in Solanum lycopersicum and show that they are functionally significant and affect their target preferences. My approach was based on small RNA sequencing and degradome data to characterize targets of these miRNAs, including the recently discovered tomato TAS5 locus. I also generated transgenic tomatoes constitutively expressing target mimic RNAs that sequester different miR482/2118 members. These tomato mimic RNA lines were less susceptible than their non-transgenic precursors to pathogens Phytophthora infestans and Pseudomonas syringae. Additionally, I investigated the role of small RNAs and their effector proteins during vegetative and reproductive development in tomato. I employed transcript and small RNA sequencing and CRISPR-Cas9 techniques of gene editing to investigate the impact of these factors in gamete viability and transposable element silencing in vegetative meristems. The results presented here provide new evidence about the extent that RNA silencing contributes to the regulation of vital processes in plants. My study primarily explores the extent to which structural differences between the members of the miR482/2118 family affect their range of action, and the use of target mimics against these miRNAs as biotechnological approach for enhancing disease resistance in highly bred cultivars.

Master of Science / Entomology / Ming-Shun Chen / Robert "Jeff" J. Whitworth / MicroRNA (miRNA) plays a role in nearly all the biological pathways and therefore may provide opportunities to develop new means to combat the Hessian fly, Mayetiola destructor, a destructive pest of wheat. This study presents a comprehensive analysis of miRNA species via deep-sequencing samples from Hessian fly second instar larvae, pupae and adults. A total of 921 unique miRNA species were identified from approximately 30 million sequence reads. Among the 921 miRNA species, only 22 were conserved among Hessian fly and other insect species, and 242 miRNA species were unique to Hessian fly, the remaining 657 share certain sequence similarities with pre-miRNA genes identified from various insect species. The abundance of the 921 miRNA species based on sequence reads varies greatly among the three analyzed stages, with 20 exclusively expressed in adults, two exclusively expressed in pupae and two exclusively expressed in second instar larvae. For miRNA species expressed in all stages, 722 were with reads lower than 10. The abundance of the remaining 199 miRNA species varied from zero to more than eight-fold differences among different stages. Putative miRNA-encoding genes were analyzed for each miRNA species. A single putative gene was identified for 594 miRNA species. Two putative genes were identified for 138 miRNA species. Three or more putative genes were identified for 86 miRNA species. The three largest families had 14, 23 and 34 putative coding genes, respectively. No gene was identified for the remaining 103 miRNA species. In addition, 1516 putative target genes were identified for 490 miRNA species based on known criteria for miRNA targets. The putative target genes are involved in a wide range of processes from nutrient metabolism to encoding effector proteins. Analysis of the expression patterns of miRNA and pre-miRNA for the miRNA family PC-5p-67443, which contains 91 genes, revealed that miRNA and pre-miRNA were expressed differently in different developmental stages, suggesting that different isogenes are regulated by different mechanisms, or pre-miRNAs had other functions in addition to as an intermediate for miRNA biogenesis. The large set of miRNA species identified here provides a foundation for future research on miRNA functions in Hessian fly and for comparative studies in other species. The differential expression patterns between a pre-miRNA and its encoded mature miRNA in a multigene family is an initial step toward understanding the functional significance of isogenes in dramatically expanded miRNA families.

abstract: Damage to the central nervous system due to spinal cord or traumatic brain injury, as well as degenerative musculoskeletal disorders such as arthritis, drastically impact the quality of life. Regeneration of complex structures is quite limited in mammals, though other vertebrates possess this ability. Lizards are the most closely related organism to humans that can regenerate de novo skeletal muscle, hyaline cartilage, spinal cord, vasculature, and skin. Progress in studying the cellular and molecular mechanisms of lizard regeneration has previously been limited by a lack of genomic resources. Building on the release of the genome of the green anole, <i>Anolis carolinensis</i>, we developed a second generation, robust RNA-Seq-based genome annotation, and performed the first transcriptomic analysis of tail regeneration in this species. In order to investigate gene expression in regenerating tissue, we performed whole transcriptome and microRNA transcriptome analysis of regenerating tail tip and base and associated tissues, identifying key genetic targets in the regenerative process. These studies have identified components of a genetic program for regeneration in the lizard that includes both developmental and adult repair mechanisms shared with mammals, indicating value in the translation of these findings to future regenerative therapies. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2015

abstract: MicroRNAs (miRNAs) are short non-coding RNAs that play key roles during metazoan development, and are frequently misregulated in human disease. MiRNAs regulate gene output by targeting degenerate elements primarily in the 3´ untranslated regions of mRNAs. MiRNAs are often deeply conserved, but have undergone drastic expansions in higher metazoans, leading to families of miRNAs with highly similar sequences. The evolutionary advantage of maintaining multiple copies of duplicated miRNAs is not well understood, nor has the distinct functions of miRNA family members been systematically studied. Furthermore, the unbiased and high-throughput discovery of targets remains a major challenge, yet is required to understand the biological function of a given miRNA. I hypothesize that duplication events grant miRNA families with enhanced regulatory capabilities, specifically through distinct targeting preferences by family members. This has relevance for our understanding of vertebrate evolution, as well disease detection and personalized medicine. To test this hypothesis, I apply a conjunction of bioinformatic and experimental approaches, and design a novel high-throughput screening platform to identify human miRNA targets. Combined with conventional approaches, this tool allows systematic testing for functional targets of human miRNAs, and the identification of novel target genes on an unprecedented scale. In this dissertation, I explore evolutionary signatures of 62 deeply conserved metazoan miRNA families, as well as the targeting preferences for several human miRNAs. I find that constraints on miRNA processing impact sequence evolution, creating evolutionary hotspots within families that guide distinct target preferences. I apply our novel screening platform to two cancer-relevant miRNAs, and identify hundreds of previously undescribed targets. I also analyze critical features of functional miRNA target sites, finding that each miRNA recognizes surprisingly distinct features of targets. To further explore the functional distinction between family members, I analyze miRNA expression patterns in multiple contexts, including mouse embryogenesis, RNA-seq data from human tissues, and cancer cell lines. Together, my results inform a model that describes the evolution of metazoan miRNAs, and suggests that highly similar miRNA family members possess distinct functions. These findings broaden our understanding of miRNA function in vertebrate evolution and development, and how their misexpression contributes to human disease. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2016