Browsing by Subject "MicroRNA"

The development and function of the nervous system relies on complex regulation of gene expression programs. MicroRNAs (miRNAs) are small RNAs that have diverse functions in mammalian development and disease. In concert with the RNA-induced silencing complex, miRNAs repress translation by binding to target mRNAs. The nervous system contains the largest proportion of miRNAs, yet few have been functionally characterized in vivo.

miR-133b is a highly conserved miRNA embedded in the sequence of 7H4, a noncoding RNA that is enriched at the neuromuscular junction (NMJ), a large synapse that is essential for eliciting muscle contraction and movement. I have found that, like 7H4, miR-133b expression is enriched at the NMJ and upregulated postnatally, coinciding with important events in synaptic maturation, including synaptic growth and elimination. Knockdown of miR-133b in postnatal muscle by electroporation of modified antisense oligonucleotides gave rise to abnormally large synapses, indicating a role for miR-133b in synaptic maturation. To specifically remove miR-133b in vivo, I generated a mouse containing a targeted deletion of the miR-133b stemloop. NMJ maturation and synapse elimination proceeded normally in miR-133b knockout mice, suggesting that miR-133b may have other functions at the synapse. The expression of 7H4 and miR-133b is upregulated following nerve transection, consistent with a role in synaptic regeneration. Indeed, NMJ reinnervation is delayed in miR-133b KO mice following nerve crush, but not nerve cut. These data suggest that miR-133b may have a specific protective function at the synapse that could be relevant to disease states, including amyotrophic lateral sclerosis (ALS), where NMJ denervation occurs following motor neuron cell death. However, loss of miR-133b did not affect survival or disease progression in the SOD1(G93A) mouse model, differentiating its role from that of miR-206, another miRNA found in 7H4.

miR-133b has recently been proposed to regulate the development and maintenance of midbrain dopaminergic (mDA) neurons. mDA neurons have critical functions in the control of movement and emotion, and their degeneration leads to motor and cognitive defects in Parkinson's disease. miR-133b is enriched in the midbrain and regulates mDA neuron differentiation in vitro by targeting Pitx3, a transcription factor required for appropriate development of substantia nigra DA neurons. However, the function of miR-133b in the intact midbrain has not been determined. miR-133b KO mice have normal numbers of midbrain dopaminergic neurons during development and aging. Moreover, dopamine neurotransmitter levels are unchanged in the striatum and other brain regions, while expression of dopaminergic genes including Pitx3 is also unaffected. Finally, miR-133b null mice display normal motor coordination and activity, suggesting that miR-133b does not play a significant role in the development or maintenance of the mDA neuron population.

Epstein-Barr virus (EBV) is a ubiquitous human gamma-herpesvirus which chronically infects >95% of the global population, and can give rise to a number of malignancies in B cells and epithelial cells. In EBV latently infected epithelial cells, such as nasopharyngeal carcinoma (NPC) and gastric carcinoma (GaCa) cells, viral protein expression is low. In contrast, a cluster of viral microRNAs (miRNAs) called miR-BARTs is highly expressed. MiRNAs are small non-coding RNAs which regulate gene expression by binding to complementary sequences in mRNAs. It is likely that miR-BARTs play a crucial role in EBV-infected epithelial cells, however a comprehensive understanding of miR-BARTs is currently lacking. Here, I present two studies utilizing the phenotypic and the target approaches, respectively, to demonstrate that miR-BARTs can inhibit apoptosis and activate the Wnt signaling pathway. To discover miR-BARTs that can inhibit apoptosis, I individually expressed miR-BARTs in the EBV- GaCa cell line AGS, and identified five miR-BARTs that conferred this phenotype. To identify pro-apoptotic genes targeted by the five anti-apoptotic miRNAs, I validated one previously published target and identified nine novel targets by performing photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) in the EBV+ NPC cell line C666. Next, I thoroughly demonstrated that the 10 candidate target genes were substantially suppressed by expression of the relevant miR-BARTs, as measured by 3’UTR-containing firefly luciferase (FLuc) expression, mRNA and protein levels, and knockdown of seven of the 10 candidate genes could suppress apoptosis, mimicking the effects of relevant miR-BARTs. On the other hand, in order to identify miR-BARTs that can activate the Wnt signaling pathway, I analyzed the PAR-CLIP data set of C666 cells and discovered nine anti-Wnt signaling targets of miR-BARTs, including seven novel genes and two pro-apoptotic genes identified above. Using FLuc 3’UTR indicator assays, I proved that the 3’UTRs of all seven newly identified anti-Wnt signaling genes were indeed targeted by the relevant miR-BARTs identified by PAR-CLIP. Utilizing a Wnt signaling FLuc reporter TOPflash which measures the Wnt signaling activation, I confirmed that expression of many miR-BARTs that target Wnt signaling inhibitors can indeed upregulate the Wnt signaling pathway. Together, my results identified and validated a substantial number of novel targets of miR-BARTs involved in apoptosis and the Wnt signaling pathway, indicating that EBV may employ miR-BARTs to heavily target these two pathways to facilitate chronic infection.

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.

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.

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.

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.

Cancer is a disease state that arises as a result of multiple alterations in signaling pathways that are critical for making key cell fate decisions in normal cells. Understanding how these pathways operate under normal circumstances, therefore, is crucial for comprehensive understanding of tumorigenic process. With Myc and E2F pathways being central components for controlling cell proliferation, an important property that defines a cancer cell, as well as expanding roles for microRNAs(miRNA) in control of gene expression, we asked if we may better understand the underlying regulatory (transcription factor, microRNA) structure that contribute to Myc and E2F pathway activities. Through integrative analysis of mRNA and miRNA expression profile, we observe a distinct regulatory pattern in which, in the case of Myc pathway, Myc-induced miRNAs were contributing to the repression of negative regulators of cell cycle, including PTEN, while in case of E2F pathway, E2F-induced miRs were forming an incoherent Feed-Forward Loop(iFFL) with a number of E2F-induced genes including cyclin E. We further demonstrate through functional studies, as well as through single cell imaging of gene expression dynamics that miRNAs, depending on the context of either Myc or E2F pathway, play distinct roles in ensuring that cell fate decisions relevant to these pathways are properly executed.

The cellular microRNA (miRNA) pathway has emerged as an important regulator of host-virus interactions. While miRNAs of viral and cellular origin have been demonstrated to modulate viral gene expression and host immune responses, reports detailing these activities in the context of mammalian retroviruses have been controversial. Using modern, high-throughput small RNA sequencing we provide evidence that the spumaretrovirus bovine foamy virus expresses high levels of viral miRNAs via noncanonical biogenesis mechanisms. In contrast, the lentivirus human immunodeficiency virus type 1 (HIV-1) does not express any viral miRNAs in a number of cellular contexts. Comprehensive analysis of miRNA binding sites in HIV-1 infected cells yielded several viral sequences that can be targeted by cellular miRNAs. However, this analysis indicated that HIV-1 transcripts are largely refractory to binding and inhibition by cellular miRNAs. In addition, we demonstrate that HIV-1 exerts minimal perturbations on cellular miRNA profiles and that viral replication is not affected by the ablation of mature cellular miRNAs. Together, these data demonstrate that the ability of retroviruses to encode miRNAs is not broadly conserved and that lentiviruses, particularly HIV-1, have evolved to avoid targeting by cellular miRNAs.

As a major component of the adaptive immune system, CD4+ T cells play a vital role in host defense and immune tolerance. The potency and accuracy of CD4+ T cell-mediated protection lie in their ability to differentiate into distinct subsets that could carry out unique duties. In this dissertation, we dissected the roles and interplays between two emerging mechanisms, miRNAs and epigenetic processes, in regulating CD4+ T cell-mediated responses. Using both gain- and loss-of-function genetic tools, we demonstrated that a miRNA cluster, miR-17-92, is critical to promote Th1 responses and suppress inducible Treg differentiation. Mechanistically, we found that through targeting Pten, miR-17-92 promotes PI3K activation. Strong TCR-PI3K activation leads to the accumulation of DNMT1, elevated CpG methylation in the foxp3 promoter, and suppression of foxp3 transcription. Furthermore, we demonstrated that an epigenetic regulator, methyl CpG binding protein 2 (MeCP2), is critical to sustain Foxp3 expression in Tregs, and to support Th1 and Th17 differentiation in conventional CD4+ T cells (Tcons). In Tregs, MeCP2 directly binds to the CNS2 region of foxp3 locus to promote its local histone H3 acetylation; while in Tcons, MeCP2 enhances the locus accessibility and transcription of miR-124, which negatively controls SOCS5 translation to support STAT1, STAT3 activation and Th1, Th17 differentiation. Overall, miRNAs and epigenetic processes may crosstalk to control CD4+ T cell differentiation and function.

MicroRNAs are key post-transcriptional regulators that have been found to play critical roles in the regulation of cellular functions. There is an emerging concept that microRNAs may be just as essential for fine-tuning physiological functions and responding to changing environments and stress conditions as for viability or development. In this dissertation, two studies are presented: The first study demonstrates a role for microRNA in the regulation of oxidative stress response in erythroid cells and the functional consequences of dysregulated microRNA expression in Sickle Cell Disease (SCD) pathobiology. The second study examines a functional role for microRNA in the cellular response to changes in cellular iron concentration. Together these studies illustrate the scope of importance of microRNAs in the coordination of cellular responses to diverse stresses.

Homozygous Sickle Cell (HbSS) erythrocytes are known to have reduced tolerance for oxidative stress, yet the basis for this phenotype has remained unknown. Here we use erythrocyte microRNA expression profiles to identify a subset of HbSS patients with higher miR-144 expression and more severe anemia. We reveal that in K562 erythroid cells and primary erythroid progenitor cells, miR-144 directly regulates NRF2, a central regulator of cellular response to oxidative stress, and modulates the oxidative stress response. We further demonstrate that increased miR-144 is associated with the reduced NRF2 levels, decreased glutathione regeneration, and attenuated antioxidant capacity found in HbSS erythroid progenitors, thereby providing a mechanism for the reduced oxidative stress tolerance and increased anemia severity seen in HbSS patients.

The post-transcriptional regulation of the IRP2 regulon in the cellular response to iron deficiency is well characterized. Here we examine the potential role for microRNA-mediated regulation in the coordinated response to cellular iron deficiency.

Immunity is broadly defined as a mechanism of protection against non-self entities, a process which must be sufficiently robust to both eliminate the initial foreign body and then be maintained over the life of the host. Life-long immunity is impossible without the development of immunological memory, of which a central component is the cellular immune system, or T cells. Cellular immunity hinges upon a naïve T cell pool of sufficient size and breadth to enable Darwinian selection of clones responsive to foreign antigens during an initial encounter. Further, the generation and maintenance of memory T cells is required for rapid clearance responses against repeated insult, and so this small memory pool must be actively maintained by pro-survival cytokine signals over the life of the host.

T cell development, function, and maintenance are regulated on a number of molecular levels through complex regulatory networks. Recently, small non-coding RNAs, miRNAs, have been observed to have profound impacts on diverse aspects of T cell biology by impeding the translation of RNA transcripts to protein. While many miRNAs have been described that alter T cell development or functional differentiation, little is known regarding the role that miRNAs have in T cell maintenance in the periphery at homeostasis.

In Chapter 3 of this dissertation, tools to study miRNA biology and function were developed. First, to understand the effect that miRNA overexpression had on T cell responses, a novel overexpression system was developed to enhance the processing efficiency and ultimate expression of a given miRNA by placing it within an alternative miRNA backbone. Next, a conditional knockout mouse system was devised to specifically delete miR-191 in a cell population expressing recombinase. This strategy was expanded to permit the selective deletion of single miRNAs from within a cluster to discern the effects of specific miRNAs that were previously inaccessible in isolation. Last, to enable the identification of potentially therapeutically viable miRNA function and/or expression modulators, a high-throughput flow cytometry-based screening system utilizing miRNA activity reporters was tested and validated. Thus, several novel and useful tools were developed to assist in the studies described in Chapter 4 and in future miRNA studies.

In Chapter 4 of this dissertation, the role of miR-191 in T cell biology was evaluated. Using tools developed in Chapter 3, miR-191 was observed to be critical for T cell survival following activation-induced cell death, while proliferation was unaffected by alterations in miR-191 expression. Loss of miR-191 led to significant decreases in the numbers of CD4+ and CD8+ T cells in the periphery lymph nodes, but this loss had no impact on the homeostatic activation of either CD4+ or CD8+ cells. These peripheral changes were not caused by gross defects in thymic development, but rather impaired STAT5 phosphorylation downstream of pro-survival cytokine signals. miR-191 does not specifically inhibit STAT5, but rather directly targets the scaffolding protein, IRS1, which in turn alters cytokine-dependent signaling. The defect in peripheral T cell maintenance was exacerbated by the presence of a Bcl-2YFP transgene, which led to even greater peripheral T cell losses in addition to developmental defects. These studies collectively demonstrate that miR-191 controls peripheral T cell maintenance by modulating homeostatic cytokine signaling through the regulation of IRS1 expression and downstream STAT5 phosphorylation.

The studies described in this dissertation collectively demonstrate that miR-191 has a profound role in the maintenance of T cells at homeostasis in the periphery. Importantly, the manipulation of miR-191 altered immune homeostasis without leading to severe immunodeficiency or autoimmunity. As much data exists on the causative agents disrupting active immune responses and the formation of immunological memory, the basic processes underlying the continued maintenance of a functioning immune system must be fully characterized to facilitate the development of methods for promoting healthy immune function throughout the life of the individual. These findings also have powerful implications for the ability of patients with modest perturbations in T cell homeostasis to effectively fight disease and respond to vaccination and may provide valuable targets for therapeutic intervention.

MicroRNAs (miRNAs) are small, single-stranded non-coding RNAs that play a crucial role in intracellular regulation of gene expression. Emerging evidence indicates that miRNAs can also be found extracellularly in various body fluids, including serum and cerebrospinal fluid (CSF), raising the possibility that these secreted miRNAs could serve as neuromodulators and disease biomarkers. Among these miRNAs, let-7b has been previously identified as a pain inducer through its actions in the peripheral nociceptive system, while TLR7 has been recognized as a critical regulator of pain and itch (pruritus). However, the role of let-7b in spinal cord synaptic transmission and its potential involvement in chronic pain and itch remains unexplored. In this thesis, our investigation commences by demonstrating that let-7b activates a non-canonical pathway of TLR7 in the presence of TRPA1 ion channels. Subsequently, we found that HEK cells and dissociated dorsal root ganglion (DRG) neurons, in which TLR7 and TRPA1 are expressed, exhibit robust calcium responses to extracellular perfusion of let-7b. Furthermore, intrathecal injection of a low dose of let-7b (1 μg) induces short-term (< 24 hours) mechanical and heat hypersensitivity. Mechanistic insights emerge from our observation that synthetic let-7b perfusion of spinal cord slices augments calcium signaling in synaptic terminals and excitatory synaptic transmission (miniature EPSCs) in spinal nociceptive neurons. These effects are contingent on TLR7 and TRPA1 ion channels. Notably, endogenous let-7b is enriched in spinal cord synaptosomes, and its expression is upregulated in DRG neurons, spinal cord tissue, and CSF in response to peripheral inflammation. To explore the role of endogenous let-7b in synaptic transmission and pain, we designed a let-7b antagomir to neutralize secreted let-7b function. Intriguingly, spinal administration of let-7b antagomir attenuates inflammation-induced mechanical pain and synaptic plasticity, suggesting an endogenous role of let-7b in inflammation-induced synaptic plasticity. Additionally, as TLR7 is expressed in spinal microglia, an intrathecal injection of high dose let-7b (10 μg) leads to persistent mechanical allodynia lasting over two weeks, and this effect in abrogated in Tlr7−/− knockout mice. This let-7b induced microgliosis is mitigated by intrathecal administration of minocycline, which suppresses let-7b-induced mechanical allodynia only in male mice but not in female mice. In a mouse cheek model, intradermal injection of let-7b induces both pain (wiping behavior) and itch (scratching behavior). Notably, endosome inhibitors selectively block let-7b-induced itch, without affecting let-7b-induced acute pain. Endosome inhibitors further suppress let-7b-induced persistent calcium increases in cultured trigeminal ganglion neurons. Our findings bring forth the concept that TLR7/TRPA1 axis activation can elicit pain and itch sensations via distinct surface and intracellular calcium signaling pathways within primary sensory neurons. Furthermore, we developed a mouse model of chronic itch induced by cutaneous T cell lymphoma (CTCL). This model is characterized by notable lymphoma growth, chronic scratching for over 60 days, neural innervation of tumor tissue, and elevated levels of let-7b in DRGs. Furthermore, intradermal or systemic administration of let-7b antagomir can alleviate CTCL-induced pruritus. Collectively, this thesis elucidates the novel molecular and cellular mechanisms of pain and itch induced by extracellular miRNA (let-7b), thereby deepening our understanding of the cell biology of primary sensory neurons and neurobiology of pain and itch.

Recent advances in nanotechnology have led to the application of nanoparticles in a wide variety of fields. In particular, anisotropic nanoparticles have shown great potential for surface-enhanced Raman scattering (SERS) detection due to their unique optical properties. Gold nanostars are a type of anisotropic nanoparticle with one of the highest SERS enhancement factors in a non-aggregated state. By utilizing the distinct characteristics of gold nanostars, new plasmonic materials for sensing, diagnostics, and therapy can be synthesized. The work described herein is divided into two main themes. The first half demonstrates the development and application of a novel label-free inverse molecular sentinel (iMS) nanoprobe for detection of microRNA biomarkers related to cancer progression as well as those related to gene expression in plants. This work also describes the initial proof-of-concept for a SERS-based electrowetting-on-dielectric (EWD) digital microfluidic platform as a diagnostic platform requiring samples of nanoliter volume. The second half demonstrates the utility of plasmonic nanoparticles for SERS imaging as well as photothermal therapy (PTT) and photodynamic therapy (PDT).

Development of accessible strategies for efficient detection of nucleic acid biomarkers is a major unmet need for applications ranging from cancer screening to agricultural biotechnology and biofuel development. MicroRNAs (miRNAs) have great promise as a new important class of biomarkers for early detection of various cancers; however, these small molecules have not been adopted into early diagnostics for clinical practice because of challenges adapting complex laboratory techniques into accessible clinical tests. In a blinded study, the surface-enhanced Raman scattering (SERS)-based plasmonics-active nanoprobes described herein, referred to as inverse molecular sentinels (iMS), demonstrated diagnostic accuracy for in vitro identification of endoscopic biopsy samples as tumor, Barrett’s esophagus or normal tissue via miRNA detection. The iMS nanoprobe technology can be designed to detect a wide range of nucleic acids for a variety of applications. In addition to medical applications, the knowledge over gene expression dynamics and location in plants is crucial for applications ranging from basic biological research to agricultural biotechnology. However, current methods are unable to provide in vivo dynamic detection of genomic targets in plants, due to the complex sample preparation needed by current methods for nucleic acids detection, which disrupt spatial and temporal resolution. We have developed a multimodal technique utilizing iMS nanoprobes for in vivo imaging and biosensing of microRNA biotargets within whole plants. This work lays the foundations for in vivo functional imaging of RNA biotargets in plants with previously unmet spatial and temporal resolution.

The prevalence of cancer has increasingly become a significant threat to human health and as such, there exists a strong need for developing novel methods for early detection and effective therapy. Gold nanostars (AuNS) with tip-enhanced plasmonics have become one of the most promising platforms in photothermal therapy (PTT) as they exhibit superior photon-to-heat conversion efficiency and can be delivered specifically to tumors. We have demonstrated that AuNS are endocytosed into multiple cancer cell lines irrespective of receptor status or drug resistance and allow for the effective photothermal ablation of tumor cells. Additionally, we demonstrate a unique in vitro preclinical model that mimics the tumor structures assumed by inflammatory breast cancer (IBC) in vivo. IBC has a unique presentation of diffuse tumor cell clusters called tumor emboli. AuNS are able to penetrate the tumor embolic core in 3D culture, allowing effective photothermal ablation of the IBC tumor emboli.

Additionally, we have furthered the development of the gold nanostar treatment platform by developing a theranostic nanoconstruct that consist of Raman-labeled gold nanostars coated with a silica shell that is loaded with photosensitizer molecules for PDT. The outer surface of the nanoconstruct was functionalized for targeting to allow for specific treatment of folate positive breast cancer. SERS detection and PDT are performed at different wavelengths, so there is no interference between the diagnostic and therapeutic modalities. Singlet oxygen generation (a measure of PDT effectiveness) was demonstrated from the drug-loaded nanocomposites. In vitro testing demonstrated the effectiveness of the nanoconstruct for targeted PDT.

The development of a functional tissue-engineered human skeletal muscle model in vitro would provide an excellent platform on which to study the process of myogenesis, various musculoskeletal disease states, and drugs and therapies for muscle toxicity. We developed a protocol to culture human skeletal muscle bundles in a fibrin hydrogel under static conditions capable of exerting active contractions. Additionally, we demonstrated the use of joint miR-133a and miR-696 inhibition for acceleration of muscle differentiation, elevation of active contractile force amplitudes, and increasing Type II myofiber formation in vitro.

The global hypothesis that motivated this research was that joint inhibition of miR-133a and miR-696 in isolated primary human skeletal myoblasts would lead to accelerated differentiation of tissue-engineered muscle constructs with higher proportion of Type I myofibers and that are capable of significantly increased active contractile forces when subjected to electrical stimulus. The proposed research tested the following specific hypotheses: (1) that HSkM would require different culture conditions than those optimal for C2C12 culture (8% equine serum in differentiation medium on uncoated substrates), as measured by miR expression, (2) that joint inhibition of miR-133a and miR-696 would result in 2D human skeletal muscle cultures with accelerated differentiation and increased Type I muscle fibers compared to control and individual inhibition of each miR, as measured by protein and gene expression, (3) that joint inhibition of miR-133a and miR-696 in this functional 3D human skeletal muscle model would result in active contraction significantly higher than control and individual inhibition by each miR, as measured by isometric force testing, and finally (4) that specific co-culture conditions could support a lamellar co-culture model in 3D of human cord blood-derived endothelial cells (hCB-ECs) and HSkM capable of active contraction, as measured by isometric force testing and immunofluorescence.

Major results of the dissertation are as follows. Culture conditions of 100 μg/mL growth factor reduced-Matrigel-coated substrates and 2% equine serum in differentiation medium were identified to improve human skeletal myoblast culture, compared to conditions optimal for C2C12 cell culture (uncoated substrates and 8% equine serum media). Liposomal transfection of human skeletal myoblasts with anti-miR-133a and anti-miR-696 led to increased protein presence of sarcomeric alpha-actinin and PGC-1alpha when cells were cultured in 2D for 2 weeks. Presence of mitochondria and distribution of fiber type did not change with miR transfection in a 2D culture. Joint inhibition also resulted in increased PPARGC1A gene expression after 2 weeks of 2D culture. For muscle bundles in 3D, results suggest there exists a myoblast seeding density threshold for the production of functional muscle. 5 x 106 myoblasts/mL did not produce active contraction, while 10 x 106 myoblasts/mL and above were successful. Of the seeding densities studied, 15 x 106 myoblasts/mL resulted in constructs that exerted the highest twitch and tetanus forces. Engineering of human skeletal muscle from transfected cells led to significant increases in force amplitude in joint inhibition compared to negative control (transfection with scrambled miR sequence). Joint inhibition in myoblasts seeded into 3D constructs led to decreased presence of slow myosin heavy chain and increased fast myosin heavy chain. Finally, co-culture of functional human skeletal muscle with human cord blood-derived endothelial cells is possible in 3.3% FBS in DMEM culture conditions, with significant increases in force amplitudes at 48 and 96 hours of co-culture.

SR proteins are a family of splicing factors involved in the regulation of both constitutive and alternative splicing of pre-mRNAs. Despite years of studies, several big questions still remain: how the expression levels of SR proteins are regulated; what are the underlying mechanisms responsible for SR proteins-mediated gene regulation; what are the physiological targets of SR proteins in vivo. In my dissertation study, I am focusing on two members of the family, SF2/ASF and SRp20, to study their functional involvement in regulating microRNA/mRNA biogenesis and their own expression.

Negative feedback regulation is a common mechanism maintaining the steady-state level of SR proteins (i.e. SC35 and SRp20), and several mechanism may be involved. In order to test if miRNAs are also involved in such negative feedbacks, small RNA sequencing was used to identify differentially expressed miRNAs after SF2/ASF overexpression in an inducible stable cell line system. Among the 40 differentially expressed miRNAs, miR-7 is particularly interesting, because it is also predicted to target SF2/ASF, which forms a negative feedback regulation. This is indeed the case as shown by luciferase reporter assay and overexpression/knocking down of miR-7 in vivo. To our knowledge, this is the first identified negative feedback circuit between a SR protein and a miRNA, which may be a general mechanism in regulating SR protein homeostasis.

To characterize the mechanism underlying SF2/ASF-enhanced miRNA biogenesis, I have employed a series of molecular and biochemical approaches to pinpoint the key molecular interactions in a minigene system, which is consist of miR-7 embedded intron and the flanking exons of its host gene. By manipulating the splicing pattern of such minigene, I have uncovered a splicing-independent function of SF2/ASF in regulating miRNA biogenesis. Directly binding between SF2/ASF protein and pri-miR-7 was demonstrated by Cross-linking and immunoprecipitation assay (CLIP) and RNA affinity purification. The precise binding site was then pinpointed by combining computational prediction and mutagenesis assay. Finally, by using in vitro pri-miRNA processing assay, I showed that SF2/ASF can promote the Drosha cleavage step of pri-miR-7 through directly association with the predicted binding site. So far, this is the first SR protein discovered, which is directly involved in miRNA biogenesis. Moreover, our preliminary data also suggested that SF2/ASF may promote miRNA biogenesis in other steps after Drosha cleavage; and different SR proteins can regulate miRNA biogenesis in a substrate-specific manner. Taken together, SR family of splicing factors may be broadly involved in miRNA biogenesis through direct interactions.

In order to study the general involvement of SR proteins in RNA biogenesis, one important step stone is to have a better profile of their targets in vivo. To achieve this, I focused on SRp20, another classic SR protein. Photoactivatable-Ribonucleoside-Enhanced Cross-linking and immunoprecipitation assay combined with deep sequencing (PAR-CLIP-seq) was used to identify the binding partners of SRp20 globally, which is subsidized by candidate gene validations. Consistent with the literature, I found that SRp20 primarily targets exonic regions for splicing regulation, and such interactions are likely to be sequence dependent on the CWWCW motif. Surprisingly, I also observed extensive binding between SRp20 and the 3' UTRs of mRNA, which may affect the choice of alternative polyadenylation sites. The underlying mechanisms are being investigated by a variety of molecular methods.

In summary, I have identified a subset of miRNAs, the expression of which can be regulated by SF2/ASF in a splicing independent manner. This is the first SR protein identified in regulating miRNA biogenesis. One of the upregulated miRNAs, miRNA-7 can form a negative feedback with SF2/ASF by negatively regulating the expression of SF2/ASF on translational level. By using PAR-CLIP method, I have identified the genome-wide binding partners of SRp20 in vivo. When SRp20 binds to the exonic regions, it potentially affects the alternative splicing patterns of nearby introns. Interestingly, the 3' end choices for a subset of genes may be regulated by SRp20 through directly binding, which may be a new mechanism for the regulation of 3' end processing.

The research presented here represents a quest to understand and address limitations in the field of skeletal muscle tissue engineering, with hopes to better understand the factors involved in producing viable engineered skeletal muscle tissue. The driving force behind this research was to address two of the many factors important in muscle cell proliferation and differentiation, toward developing mature and functional bioartificial skeletal muscles (BAMs). Our work focused on understanding the individual effects of mechanical stimulation and microRNAs (miRNAs), as well as the synergistic relationship between the two factors. We hypothesized that (1) myoblast proliferation and differentiation are modulated by mechanical stimulation via temporally regulated miRNAs and that (2) modulating these miRNAs can enhance skeletal muscle function in a 3D tissue-engineered system.

We first established a BAM system using C2C12 mouse myoblasts in a collagen gel, showing that these cells were able to produce mature sarcomeres when cultured under steady, passive tension for up to 36 days. Staining muscle-specific proteins and electron microscopy showed distinct striations and myofiber organization as early as 6 days, post-differentiation. At 33 days, cultures contained collagen fibers and showed localization of paxillin at the fiber termini, suggesting that myotendinous junctions were forming.

We then focused on the effects of mechanical stimulation on C2C12 myoblasts in a more simple, 2D system. In particular, we assessed miRNA and muscle-specific gene expression over time and in response to two cyclic stretch regimens using miRNA microarray technology and quantitative real time RT-PCR. Both miRNAs and certain genes, such as SRF and Mef2c, had differential responses to the two regimens. Over-expression and inhibition studies of one muscle-specific miRNA, miR-1, abrogated the stretch response and suggest that a balancing mechanism is in place to avoid large fluctuations in miRNA levels.

Finally, since miRNA modulation quenched the stretch-mediated response in myoblasts, we chose to examine 3D BAM function when miRNA levels were altered to promote differentiation. Using the same collagen gel model established previously, a muscle-specific miRNA, miR-133, known to promote proliferation, was transiently inhibited (anti-miR-133) to encourage differentiation. Forces in the anti-miR-133 BAMs were, on average, 20% higher over the negative control. Further, myofiber diameters were significantly greater and striations were more organized in the anti-miR-133 BAMs, suggesting that transient, exogenous delivery of miRNAs may be a viable approach to create a more fully differentiated muscle.

Dysregulated inflammation underlies the pathogenesis of a myriad of human diseases ranging from cancer to autoimmunity. As coordinators, executers and sentinels of host immunity, T cells represent a compelling target population for immune-modulation. In fact, the antigen-specificity, cytotoxicity and promise of long-lived of immune-protection make T cells ideal vehicles for cancer immunotherapy. Interventions for autoimmune disorders, on the other hand, aim to dampen T cell-mediated inflammation and promote their regulatory functions. Although significant strides have been made in targeting T cells for immune-modulation, current approaches remain less than ideal and leave room for improvement. In this dissertation, I seek to improve on current T cell-targeted immunotherapies, by identifying and preclinically characterizing their mechanisms of action and in vivo therapeutic efficacy.

CD8+ cytotoxic T cells have potent antitumor activity and therefore are leading candidates for use in cancer immunotherapy. The application of CD8+ T cells for clinical use has been limited by the susceptibility of ex vivo-expanded CD8+ T cells to become dysfunctional in response to immunosuppressive microenvironments. To enhance the efficacy of adoptive cell transfer therapy (ACT), we established a novel microRNA-targeting approach that augments CTL cytotoxicity and preserves immunocompetence. Specifically, we screened for miRNAs that modulate cytotoxicity and identified miR-23a as a strong functional repressor of the transcription factor Blimp-1, which promotes CTL cytotoxicity and effector cell differentiation. In a cohort of advanced lung cancer patients, miR-23a was upregulated in tumor-infiltrating CD8+ T cells, and its expression correlated with impaired antitumor potential of patient CD8+ T cells. We determined that tumor-derived TGF-β directly suppresses CD8+ T cell immune function by elevating miR-23a and downregulating Blimp-1. Functional blockade of miR-23a in human CD8+ T cells enhanced granzyme B expression; and in mice with established tumors, immunotherapy with just a small number of tumor-specific CD8+ T cells in which miR-23a was inhibited robustly hindered tumor progression. Together, our findings provide a miRNA-based strategy that subverts the immunosuppression of CD8+ T cells that is often observed during adoptive cell transfer tumor immunotherapy and identify a TGFβ-mediated tumor immune-evasion pathway.

Having established that miR-23a-inhibition can enhance the quality and functional-resilience of anti-tumor CD8+ T cells, especially within the immune-suppressive tumor microenvironment, we went on to interrogate the translational applicability of this strategy in the context of chimeric antigen receptor (CAR)-modified CD8+ T cells. Although CAR T cells hold immense promise for ACT, CAR T cells are not completely curative due to their in vivo functional suppression by immune barriers ‒ such as TGFβ ‒ within the tumor microenvironment. Since TGFβ poses a substantial immune barrier in the tumor microenvironment, we sought to investigate whether inhibiting miR-23a in CAR T cells can confer immune-competence to afford enhanced tumor clearance. To this end, we retrovirally transduced wildtype and miR-23a-deficient CD8+ T cells with the EGFRvIII-CAR, which targets the PepvIII tumor-specific epitope expressed by glioblastomas (GBM). Our in vitro studies demonstrated that while wildtype EGFRvIII-CAR T cells were vulnerable to functional suppression by TGFβ, miR-23a abrogation rendered EGFRvIII-CAR T cells immune-resistant to TGFβ. Rigorous preclinical studies are currently underway to evaluate the efficacy of miR-23a-deficient EGFRvIII-CAR T cells for GBM immunotherapy.

Lastly, we explored novel immune-suppressive therapies by the biological characterization of pharmacological agents that could target T cells. Although immune-suppressive drugs are classical therapies for a wide range of autoimmune diseases, they are accompanied by severe adverse effects. This motivated our search for novel immune-suppressive agents that are efficacious and lack undesirable side effects. To this end, we explored the potential utility of subglutinol A, a natural product isolated from the endophytic fungus Fusarium subglutinans. We showed that subglutinol A exerts multimodal immune-suppressive effects on activated T cells in vitro: subglutinol A effectively blocked T cell proliferation and survival, while profoundly inhibiting pro-inflammatory IFNγ and IL-17 production by fully-differentiated effector Th1 and Th17 cells. Our data further revealed that subglutinol A might exert its anti-inflammatory effects by exacerbating mitochondrial damage in T cells, but not in innate immune cells or fibroblasts. Additionally, we demonstrated that subglutinol A significantly reduced lymphocytic infiltration into the footpad and ameliorated footpad swelling in the mouse model of Th1-driven delayed-type hypersensitivity. These results suggest the potential of subglutinol A as a novel therapeutic for inflammatory diseases.

Cancer metastasis is the cause of about 90% of cancer patients' deaths. Despite significant improvements in the past three decades in understanding the molecular bases of oncogenic transformation of cancer cells, little is known about the molecular mechanisms underlying tumour cells' alteration of their microenvironment, entrance into the circulation, and colonization of distant organs. In recent years, accumulating evidence has indicated that tumour microenvironment, which consists of a variety of cell types and extracellular matrix components，plays an important role in regulating the metastatic abilities of carcinoma cells. Co-opted by cancer cells, those stromal cells promote tumour progression via multiple mechanisms, including enhancement of tumour invasiveness, elevation of angiogenesis, and suppression of immune surveillance activity.

Using a series of human breast cancer cell lines with different metastatic potentials in vivo, we performed an unbiased screen examining expression of miRNAs, and found that miR-126 and miR-126*, whose expression are regulated by methylation of the promoter of their host gene Egfl7 inside tumour cells, were significantly negatively correlated with metastatic potential. Using both mouse xenograft models and in vitro assays, we showed that this pair of miRNAs suppressed breast cancer metastasis through shaping the tumour microenvironment without changing tumour cell autonomous properties. Specifically, miR-126 and miR-126* act independently to suppress the sequential recruitment of mesenchymal stem cells (MSCs) and inflammatory monocytes into the primary tumour stroma, consequently inhibiting lung metastasis by breast tumour cells. Mechanistically, these miRNAs directly inhibit the production of stromal cell-derived factor-1 alpha (Sdf-1α, also known as Cxcl12), and indirectly suppress the expression of chemokine (C-C motif) ligand 2 (Ccl2) by the cancer cells within the tumour mass in an Sdf-1α-dependent manner. In addition, in contrast with the majority of reports which have shown incorporation of only the guiding strand of the miRNA duplex into the mRNA-targeting RNA induced silencing complex (RISC), both strands of the miR-126 RNA duplex are maintained at a similar level and suppress Sdf-1α expression independently.

Collectively, we have determined a dynamic process by which the composition of the primary tumour microenvironment could be altered via a change in the expression of two tumour-suppressive miRNAs derived from a single miRNA precursor to favor metastasis by breast cancer cells. Importantly, this work provides a prominent mechanism to explain the clinical correlation between reduced expression of miR-126/126* and poor metastasis-free survival of breast cancer patients.

microRNAs (miRNAs) downregulate the expression of numerous mRNAs and are involved in almost every biological process where they have been examined. Inherent sequence or cis-elements located in mRNA termini and 5' and 3' UTRs likewise influence post-transcriptional gene regulation. We delineate the relative importance of the 5' m7G-cap, the 3' poly(A) tail, and Internal Ribosome Entry Sites (IRESs) in miRNA-mediated repression. mRNA targets must contain a m7G-cap to be repressed, are repressed to a greater extent when containing a poly(A) tail, and are not precluded from repression when translating via an IRES.

miRNAs can inhibit translation and / or induce mRNA decay. While the core effector proteins are established, mechanistic details of how miRNAs interfere with mRNA translation and stability remain elusive. Contrary to the repressive effects of miRNAs, the poly(A)-binding protein (PABP) (through binding to the poly(A) tail and eIF4G) can increase both translation and mRNA stability independently. We elucidate a functional role for the PABP in miRNA repression; manipulation of `active' PABP levels affects repression conversely in part by inhibiting miRNA-induced deadenylation. Furthermore, we find that expression changes in the PABP binding partner PABP interacting protein 2 (Paip2) modulates both miRNA repression and PABP protein complex formation. Additionally, we establish Paip2 as a bona fide miR-128 target, and demonstrate miR-128 de-repression of non-miR-128 target mRNAs through this targeting event.