Dissertation (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2007. / Vita. Bibliography: p.164-178.

Thesis (Ph. D.)--Case Western Reserve University, 2007. / [School of Medicine] Department of Biochemistry. Includes bibliographical references. Available online via OhioLINK's ETD Center.

Alternative pre-messenger RNA splicing affects a majority of human genes and plays important roles in development and disease. Alternative splicing (AS) events conserved since the divergence of human and mouse are likely of primary biological importance, but relatively few such events are known. Here we describe sequence features that distinguish exons subject to evolutionarily conserved AS, which we call 'alternative-conserved exons' (ACEs) from other orthologous human/mouse exons, and integrate these features into an exon classification algorithm, ACEScan. Genome-wide analysis of annotated orthologous human-mouse exon pairs identified ~2,000 predicted ACEs. Alternative splicing was verified in both human and mouse tissues using an RT-PCR-sequencing protocol for 21 of 30 (70%) predicted ACEs tested, supporting the validity of a majority of ACEScan predictions. By contrast, AS was observed in mouse tissues for only 2 of 15 (13%) tested exons which had EST or cDNA evidence of AS in human but were not predicted ACEs, and was never observed for eleven negative control exons in human or mouse tissues. Predicted ACEs were much more likely to preserve reading frame, and less likely to disrupt protein domains than other AS events, and were enriched in genes expressed in the brain and in genes involved in transcriptional regulation, RNA processing and development. Our results also imply that the vast majority of AS events represented in the human EST databases are not conserved in mouse, and therefore may represent aberrant, disease- or allele-specific, or highly lineage-restricted splicing events.

Rhabdomyosarcoma (RMS) is a highly malignant pediatric cancer that is the most common form of soft tissue tumors in children. RMS cells have many features of skeletal muscle cells, yet do not differentiate. Thus, our studies have focused on the molecular defects present in these cells that block myogenesis. We have found MEF2D is absent in RMS cell lines representing both major subtypes of RMS and primary cells derived from an embryonal RMS mice model. We have shown that the down regulation of MEF2D is a major cause for the failure of RMS cells to differentiate. We find MEF2D cannot bind to muscle specific gene promoters. Exogenous expression of MEF2D activates muscle specific luciferase constructs, upregulates p21 expression and increases muscle specific gene expression including the expression of myosin heavy chain, a marker for skeletal muscle differentiation. Restoring expression of MEF2D also inhibits proliferation, cell motility, anchorage independent growth in vitro, and tumor growth in vivo by xenograft assay. We also have found MEF2C is deregulated in rhabdomyosarcoma with the aberrant alternative splicing. We have shown that exon α in MEF2C is aberrantly alternatively spliced in RMS cells, with the ratio of α2/α1 being highly downregulated in RMS cells compared with normal myoblasts. We find that MEF2Cα1 is the ubiquitously expressed isoform which exhibits no myogenic activity and that MEF2Cα2, the muscle specific MEF2C isoform, is required for efficient differentiation. Compared with MEF2Cα2, MEF2Cα1 more strongly interacts with and recruits HDAC5 to myogenic gene promoters to repress muscle specific genes. Overexpression of the MEF2Cα2 isoform in RMS cells increases myogenic activity and promotes differentiation in RMS cells. We have also identified a serine protein kinase, SRPK3, which is downregulated in RMS cells and found that expression of SRPK3 promoted the splicing of the MEF2Cα2 isoform and induced differentiation. Restoration of either MEF2Cα2 or SPRK3 inhibited both proliferation and anchorage independent growth of RMS cells. The NAC complex performs many diverse biological functions, and the deregulation of its subunits has been correlated with many cancers. We sought to understand the function of the NAC complex in normal myogenesis and tumor progression in rhabdomyosarcoma cells. We found that the muscle specific subunit of the NAC complex, skNAC, which is the alternatively spliced isoform of NACα, was induced in normal cells and downregulated in RMS cells, while BTF3, also known as NACβ, was induced in normal cells and severely downregulated in RMS cells. We also showed that skNAC associated with muscle specific promoters together with BTF3 in differentiated normal cells, and this association was dependent on the expression of BTF3. We further investigated the involvement of skNAC in RMS progression. We found that the muscle specific expressed methyltransferase Smyd1 was nuclear localized in RMS cells and its interaction partner skNAC was switched with corepressors (HDAC1 and TBX2). We also confirmed the expression of skNAC was regulated by the splicing factor kinase SRPK3 and overexpression of SPRK3 induced skNAC expression and muscle differentiation in RMS cells. We also confirmed the overexpression of BTF3 in patient RMS tumors and depletion of BTF3 induced apoptosis in RMS cells and decrease RMS cell survival. BTF3 depletion also sensitized TRAIL induced cell apoptosis in RMS cells. However, BTF3 played a different role in normal cells. Deletion of BTF3 in C2C12 cells does not induce cell apoptosis, which suggests BTF3 functions as an anti-apoptosis factor in RMS cells and could be used as a cancer specific therapeutic target in RMS cells.

O splicing alternativo é um processo pelo qual os exons de um transcrito primário são ligados de diferentes maneiras durante o processamento do RNA, levando à síntese de proteínas distintas. Compreende um importante mecanismo na expressão gênica de eucariotos, responsável pelo aumento da diversidade proteômica e, portanto da capacidade codificante do genoma. Diferentes mecanismos parecem afetar a regulação do splicing alternativo, incluindo estresse metabólico. No presente estudo, foi realizada uma análise detalhada de sequências ORESTES de tecidos de cabeça e pescoço. Essa análise revelou que o ganho de sequências exônicas é mais freqüente que sua perda, e que a regra GT/AG é predominante em sítios de splicing. Nós observamos que o splicing alternativo geralmente não altera a matriz de leitura, mas pode afetar um domínio protéico e remover ou adicionar novos sítios de fosforilação e glicosilação. Elementos reguladores potenciais e elementos repetitivos foram freqüentes nas sequências alternativas e nas suas vizinhas. A expressão de isoformas de splicing potenciais foi investigada em diferentes tecidos, incluindo sob condições de estresse. Foram validados cerca de 50 eventos de splicing novos em células normais e tumorais. Diversas variantes, tais como aquelas dos genes HNRNPK, ACTN1, BAT3, CEP192, MPV17, PDK1, PRKAR1A, RAG1AP1 e TRIP6 mostraram padrões de expressão distintos em diferentes tipos celulares, em amostras normais e tumorais de pacientes com carcinoma de cabeça e pescoço e, em alguns casos, em diferentes estágios do tumor. Também foi validado um transcrito novo do gene RIPK2, responsável por codificar uma quinase de serine/treonine que ativa a via de sinalização NF-kB, e foi observada uma mudança na expressão dessa variante em resposta ao estresse térmico in vitro. Ainda não está claramente definido se o splicing alternativo é causa ou conseqüência do processo neoplásico. Nossos dados adicionam informações novas a esse tópico e fornecem alguns exemplos que evidenciam a importância do processamento do RNA na regulação da expressão gênica, tanto em condições normais como de doença. / Alternative splicing is a process by which the exons of the primary gene transcript are linked in different ways during RNA processing resulting in distinctive proteins. It is an important mechanism in eukaryotic gene expression that enhances proteome diversity and, therefore, the coding capacity of the genome. Different mechanisms seem affect alternative splicing regulation, including metabolic stresses. In the present study, a detailed informatics analysis of ORESTES sequences from head and neck tissues was performed. This in silico analysis revealed that gain of exon sequences is more frequent than exon skipping and GT/AG rule is predominant in splice sites. We observed that alternative splicing usually does not alter the reading frame but may disrupt a protein domain and remove or add new phosphorylation and glycosylation sites. Repetitive and potential regulator elements were frequent in the alternative sequences or in their neighbors. The expression of putative splicing isoforms was investigated in different tissues, including upon stress conditions. We validated approximately 50 new splicing events in normal and tumor cells. Several variants, such as those from HNRNPK, ACTN1, BAT3, CEP192, MPV17, PDK1, PRKAR1A, RAG1AP1 and TRIP6 genes showed distinctive expression pattern in different cell types, in normal and cancer samples from head and neck carcinoma patients and, in some cases, in different tumor stages. We also validated a new transcript of RIPK2 gene, which codes a serine/threonine kinase that activates the NF-kB pathway, and observed a shift in the expression of this variant as a response to temperature stress in vitro. It is currently not clear whether alternative splicing is the cause or the consequence of the neoplastic process. Our data add new information to this topic and provide some examples on the importance of RNA processing in gene expression regulation, both in normal and disease conditions.

The misregulation of post-transcriptional mechanisms has been linked to the development and progression of numerous human diseases, in particular neurological disorders and cancer. Investigating these misregulated RNA pathways is essential to fully understand the disease mechanisms, identify novel biomarkers, and to develop effective therapies. In this thesis, I present three manuscripts that investigate the mechanisms behind the post-transcriptional misregulation of RNA in human disease, with a focus on pre-mRNA splicing. In the first manuscript (Bondy-Chorney et al., 2016a), we investigated the role of Staufen1 (Stau1) in splicing regulation in the neuromuscular disorder Myotonic Dystrophy Type 1 (DM1). Here we report the first insights into the mechanism that Stau1 uses to regulate the alternative splicing of INSR exon 11 through an interaction with Alu elements located in intron 10. Moreover, using a high-throughput RT-PCR screen, we uncovered a number of additional Stau1-regulated alternative splicing events in both wild-type and DM1 myoblast cell lines. As Stau1 is known to be aberrantly upregulated in DM1 skeletal muscle, our findings suggest that Stau1 acts as a disease modifier in this disorder. The second manuscript (Sanchez, Bondy-Chorney et al., 2015), describes a novel role of the protein methyltransferase Coactivator-Associated Methyltransferase-1 (CARM1), a protein found to be overexpressed in Spinal Muscular Atrophy (SMA). We found that CARM1 can act as a mediator in the nonsense-mediated decay pathway (NMD) and associated UPF1 to promoted its occupancy on PTC-containing transcripts. We identified a subset of natural non-PTC containing NMD targets that were dependent on CARM1, a number of which were misregulated in SMA. This work uncovered a novel role for CARM1 in the NMD pathway and revealed that defective targeting of PTC-containing mRNAs should be included in the complex array of molecular defects associated with SMA. Finally, the third manuscript (Bondy-Chorney et al., – in prep) examines the alternative iv splicing regulation of the Protein Arginine Methyltransferase PRMT1 exon 2, an event shown to alter the growth, survival, and invasion of breast cancer cells. Here, we used an RNA interference (RNAi) RT-PCR screen to uncover several splicing proteins that regulate the inclusion of exon 2, several of which we found to be misregulated in a panel of breast cancer cell lines and patient tumours. These findings confirmed that the inclusion of PRMT1 exon 2 was regulated by alternative splicing via splicing factors that are altered in breast cancer. Moreover, depletion of one of these splicing factors, RALY, resulted in a decrease in the motility and invasive potential of an aggressive breast cancer cell line. These three manuscripts represent a collection of work focused on elucidating the mechanisms involved in post-transcriptional misregulation of RNA in three diverse human diseases. Taken together, the data presented here highlight the broad impact that proteins, such as Stau1 and CARM1, can have in neuromuscular disorders. Moreover, we also uncovered novel misregulation of splicing proteins that alter alternative splicing patterns in breast cancer. Elucidating these mechanisms is of the highest importance in order to identify potential new and effective treatment avenues.

Abstract Type IV collagen is only found in basement membranes, where it is the major structural component, providing a framework for the binding of other basement membrane components and a substratum for cells. The type IV collagen molecule is triple-helical and composed of three a chains which exist as six distinct forms (α1 - α6). Abnormalities in this basement membrane collagen structure and function are connected to both inherited and acquired diseases. Alport syndrome is a hereditary kidney disease associated with extrarenal complications, such as sensorineural deafness and eye abnormalities. The disease is caused by mutations in the COL4A3, COL4A4 and COL4A5 genes, coding for the type IV collagen α3, α4 and α5 chain genes, respectively. About 85% of the Alport syndrome cases are X-linked dominant, caused by mutations in the COL4A5 gene. In order to develop a basis for automated mutation analysis of the COL4A5 gene, previously unknown intron sequences flanking exons 2 and 37 were determined. Intron sequences flanking the other 49 exons were expanded from 35 to 190, and additionally, two novel 9 bp exons (exons 41A and 41B) were characterized in the large intron 41. In addition to optimization of the PCR amplification and sequencing conditions for all 51 exons and exon flanking sequences, optimization for the 820 bp promoter region and for the two novel exons was performed as well. Mutations were found in 79 unrelated patients of the 107 studied. This gives a high mutation detection rate of almost 75% in comparison with 50%, at its best, in other extensive mutation analyses of the COL4A5 gene using SSCP analysis. None of the mutations involved the promoter region or exons 41A and 41B. Circulating antibodies against basement membrane components have been recognized in some autoimmune diseases. Goodpasture syndrome is a rare autoimmune disease characterized by progressive glomerulonephritis and pulmonary hemorrhage. The target of the antibodies in this disease has been shown to be the noncollagenous NC1 domain of type IV collagen α3 chain. For unknown reasons, a minority of Alport syndrome patients also develops antibodies against α3 and α5 chains after renal transplantation with manifestation of severe anti-GBM disease. In order to investigate the antibodies both in Goodpasture and Alport syndrome, the NC1 domains of all six type IV collagen chains were produced as recombinant proteins in bacterial and mammalian expression systems, and an ELISA method was developed for antibody detection. Antibodies were found in both syndromes, interestingly also in Alport syndrome patients without the anti-GBM disease. The results of this work have a significant clinical value by providing for the first time complete, effective DNA-based analysis of all exon/intron and promoter regions of the COL4A5 gene in Alport syndrome.

Members of the Mef2 transcription factor family are extensively studied within the muscle field for their ability to cooperate with the myogenic regulatory factors MyoD and myogenin during muscle differentiation. Although it is known that Mef2 pre-mRNAs undergo alternative splicing, the different splice forms have not been functionally annotated. In this thesis, my studies aimed to characterize three Mef2D splice forms: MEF2Dα'β, MEF2Dαβ, MEF2Dαø. Our results show that MEF2D splice forms can be differentially phosphorylated by p38 MAPK and PKA in vitro. Gene expression analysis using cell lines over-expressing each Mef2D splice form suggests that they can differentially activate desmin, myosin heavy chain and myogenin expression. Mass spectrometry analyses from our pull-down assays reveal known and novel MEF2D binding partners. Our work suggests that Mef2D splice forms have overlapping but distinct roles and provides new insight into the importance of Mef2D alternative splicing during skeletal myogenesis.

Indiana University-Purdue University Indianapolis (IUPUI) / The protein kinase General control non-derepressible-2 (GCN2) is a key regulator of the Integrated stress response that responds to various stress signals, including nutritional deprivation. As a result of high levels of uncharged tRNAs during amino acid depletion, GCN2 phosphorylates serine-51 of the α subunit of eukaryotic initiation factor-2 (eIF2), a translation factor that delivers initiator tRNA to ribosomes. Phosphorylation of eIF2α inhibits general translation, which conserves energy and nutrients and facilitates reprogramming of gene expression for remediation of stress damage. Phosphorylation of eIF2α also directs preferential translation of specific transcription factors, such as ATF4. ATF4 reprograms gene expression to alleviate stress damage; however, under chronic stress, ATF4 directs the transcriptional expression of CHOP, which can trigger apoptosis. Because multiple stresses can induce eIF2α phosphorylation and translational control in mammals, this pathway is referred to as the Integrated stress response. GCN2 and CHOP are subject to alternative splicing that results in multiple transcripts that differ in the 5'-end of the gene transcripts. However, the effect of the different GCN2 and CHOP isoforms on their function and regulation have not been investigated. Our data suggests that GCN2 is alternatively spliced into five different transcripts and the beta isoform of GCN2 is most abundant. Also alternative splicing of CHOP creates two CHOP transcripts with different 5'-leaders encoding inhibitory upstream open reading frames that are critical for translational control of CHOP during stress. This study suggests that alternative splicing can play an integral role in the implementation and regulation of key factors in the Integrated stress response.

Indiana University-Purdue University Indianapolis (IUPUI) / Alternative RNA splicing is an important means of genetic control and transcriptome diversity. Alternative splicing events are frequently studied independently, and coordinated splicing controlled by common factors is often overlooked: The molecular mechanisms by which splicing regulators promote or repress specific pre-mRNA processing are still not yet well understood. It is well known that splicing factors can regulate splicing in a context-dependent manner, and the search for modulation of splicing factor activity via direct or indirect mechanisms is a worthwhile pursuit towards explaining context-dependent activity. We hypothesized that the combined analysis of hundreds of consortium RNA-seq datasets could identify trans-acting “modulators” whose expression is correlated with differential effects of a splicing factor on its target splice events in mRNAs. We first tested a genome-wide approach to identify relationships between RNA-binding proteins and their inferred modulators in kidney cancer. We then applied a more targeted approach to identify novel modulators of splicing factor SRSF1 function over dozens of its intron retention splicing targets in a neurological context using hundreds of dorsolateral prefrontal cortex samples. Our hypothesized model was further strengthened with the incorporation of genetic variants to impute gene expression in a Mendelian randomization-based approach. The modulators of intron retention splicing we identified may be associated with risk variants linked to Alzheimer’s Disease, among other neurological disorders, to explain disease-causing splicing mechanisms. Our strategy can be widely used to identify modulators of RNA-binding proteins involved in tissue-specific alternative splicing.