Exon sequence is required for regulated RNA splicing of the human fibroblast growth factor receptor-1 alpha-exon

Why should we still care about oncogenes?

Although oncogenes and their transformation mechanisms have been known for 30 years, we are just now using our understanding of protein function to abrogate the activity of these genes to block cancer growth. The advent of specific small-molecule inhibitors has been a tremendous step in the fight against cancer and their main targets are the cellular counterparts of viral oncogenes. The best-known example of a molecular therapeutic is Gleevec (imatinib). In the early 1990s, IFN-alpha treatment produced a sustained cytologic response in approximately 33% of chronic myelogenous leukemia patients. Today, with Gleevec targeting the kinase activity of the proto-oncogene abl, the hematologic response rate in chronic myelogenous leukemia patients is 95% with 89% progression-free survival at 18 months. There are still drawbacks to the new therapies, such as drug resistance after a period of treatment, but the drawbacks are being studied experimentally. New drugs and combination therapies are being designed that will bypass the resistance mechanisms.

Enhancer-dependent splicing of FGFR1 alpha-exon is repressed by RNA interference-mediated down-regulation of SRp55

The FGFR1 gene transcript is alternatively processed to produce functionally different receptor forms. Previously, we identified a 69-nucleotide exonic splicing enhancer (ESE) required for alpha-exon inclusion in JEG3 cells. In the present study, we found that this sequence is composed of three independent elements, two smaller ESE sequences flanking an exonic splicing silencer sequence. Ultraviolet cross-linking and immunoprecipitation identified ESE-specific binding of the splicing regulator SRp55. A RNA interference-mediated decrease in SRp55 confirmed the significance of this interaction. There was a 6- to 14-fold decrease in exon inclusion on ablation of SRp55. In SNB19 glioblastoma cells, which normally skip this exon, SRp55 was also demonstrated to play a role in exon inclusion after the removal of intronic splicing silencer sequences. These observations indicate that SRp55 plays a major role in maintaining normal FGFR1 alpha-exon inclusion, which is subject to dominant intronic splicing silencer-mediated and exonic splicing silencer-mediated inhibition in SNB19 cells.

Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression

Intron removal from a pre-mRNA by RNA splicing was once thought to be controlled mainly by intron splicing signals. However, viral and other eukaryotic RNA exon sequences have recently been found to regulate RNA splicing, polyadenylation, export, and nonsense-mediated RNA decay in addition to their coding function. Regulation of alternative RNA splicing by exon sequences is largely attributable to the presence of two major cis-acting elements in the regulated exons, the exonic splicing enhancer (ESE) and the suppressor or silencer (ESS). Two types of ESEs have been verified from more than 50 genes or exons: purine-rich ESEs, which are the more common, and non-purine-rich ESEs. In contrast, the sequences of ESSs identified in approximately 20 genes or exons are highly diverse and show little similarity to each other. Through interactions with cellular splicing factors, an ESE or ESS determines whether or not a regulated splice site, usually an upstream 3' splice site, will be used for RNA splicing. However, how these elements function precisely in selecting a regulated splice site is only partially understood. The balance between positive and negative regulation of splice site selection likely depends on the cis-element's identity and changes in cellular splicing factors under physiological or pathological conditions.

Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression

Intron removal from a pre-mRNA by RNA splicing was once thought to be controlled mainly by intron splicing signals. However, viral and other eukaryotic RNA exon sequences have recently been found to regulate RNA splicing, polyadenylation, export, and nonsense-mediated RNA decay in addition to their coding function. Regulation of alternative RNA splicing by exon sequences is largely attributable to the presence of two major cis-acting elements in the regulated exons, the exonic splicing enhancer (ESE) and the suppressor or silencer (ESS). Two types of ESEs have been verified from more than 50 genes or exons: purine-rich ESEs, which are the more common, and non-purine-rich ESEs. In contrast, the sequences of ESSs identified in approximately 20 genes or exons are highly diverse and show little similarity to each other. Through interactions with cellular splicing factors, an ESE or ESS determines whether or not a regulated splice site, usually an upstream 3' splice site, will be used for RNA splicing. However, how these elements function precisely in selecting a regulated splice site is only partially understood. The balance between positive and negative regulation of splice site selection likely depends on the cis-element's identity and changes in cellular splicing factors under physiological or pathological conditions.

Roles of hnRNP A1, SR proteins, and p68 helicase in c-H-ras alternative splicing regulation

Human ras genes play central roles in coupling extracellular signals with complex intracellular networks controlling proliferation, differentiation, and apoptosis, among others processes. c-H-ras pre-mRNA can be alternatively processed into two mRNAs due to the inclusion or exclusion of the alternative exon IDX; this renders two proteins, p21H-Ras and p19H-RasIDX, which differ only at the carboxy terminus. Here, we have characterized some of the cis-acting sequences and trans-acting factors regulating IDX splicing. A downstream intronic silencer sequence (rasISS1), acting in concert with IDX, negatively regulates upstream intron splicing. This effect is mediated, at least in part, by the binding of hnRNP A1. Depletion and add-back experiments in nuclear extracts have confirmed hnRNP A1's inhibitory role in IDX splicing. Moreover, the addition of two SR proteins, SC35 and SRp40, can counteract this inhibition by strongly promoting the splicing of the upstream intron both in vivo and in vitro. Further, the RNA-dependent helicase p68 is also associated with both IDX and rasISS1 RNA, and suppression of p68 expression in HeLa cells by RNAi experiments results in a marked increase of IDX inclusion in the endogenous mRNA, suggesting a role for this protein in alternative splicing regulation.

Ligand activation of alternatively spliced fibroblast growth factor receptor-1 modulates pancreatic adenocarcinoma cell malignancy

Pancreatic adenocarcinoma continues to be a devastating tumor (28,000 new cases per year in the United States; 10% 2-year survival). Pancreatic adenocarcinoma frequently (90% of the time) overexpresses fibroblast growth factor ligands (FGF-1 and FGF-2) and alternatively spliced high-affinity receptors (FGFR-1beta) (FGFR-1alpha was previously found in normal pancreatic tissue). To study the significance of this observation in vitro, PANC-1 cells were stably transfected via the pMEXneo vector containing FGFR-1alpha (PANC-1alpha) or FGFR-1beta (PANC-1beta) isoforms. Cells were treated with 1 mg/ml of 5-fluorouracil. Cells were evaluated for growth inhibition, apoptosis (propidium iodide staining and flow cytometry, caspase 3 activation) and for Bcl-x(L)/BAX expression (by Western blot analysis). In vivo, 7 x 10(6) cells of each isoform were injected into nude Balb/c mice for xenograft formation (N = 10). Compared to PANC-1beta (9%) in vitro, 5-fluorouracil-induced death was significantly (P < 0.05) increased in PANC-1alpha (20%) at 24 hours. Increased cell death in PANC-1alpha was mediated by activated caspase 3 and was correlated with decreased expression of Bcl-x(L)/BAX. In vivo, PANC-1beta readily demonstrated formation of tumor xenograft at 2 weeks, whereas PANC-1alpha did not form tumors. Alternative splicing of FGFR-1 to the beta isoform appears to correlate with pancreatic adenocarcinoma cell growth in vivo and resistance to chemotherapy. Inhibition of FGFR-1 splicing or overexpression of FGFR-1alpha inhibits pancreatic adenocarcinoma cell growth in vivo and restores cytotoxic responses to chemotherapy, thereby suggesting the basis of rational interventional strategies for this devastating tumor.

Alternative ribonucleic acid processing in endocrine systems

Alternative RNA processing is a mechanism for creation of protein diversity through selective inclusion or exclusion of RNA sequence during posttranscriptional processing. More than one-third of human pre-mRNAs undergo alternative RNA processing modification, making this a ubiquitous biological process. The protein isoforms produced have distinct and sometimes opposite functions, underscoring the importance of this process. This review focuses on important endocrine genes regulated by alternative RNA processing. We discuss how diverse events such as spermatogenesis or GH action are regulated by this process. We focus on several endocrine (calcitonin/calcitonin gene-related peptide) and nonendocrine (Drosophila doublesex and P-element and mouse c-src) examples to highlight recent progress in the elucidation of molecular mechanisms regulating this process. Finally, we outline methods (model systems and techniques) used by investigators in this field to study processing of individual pre-mRNAS:

Redundant intronic repressors function to inhibit fibroblast growth factor receptor-1 alpha-exon recognition in glioblastoma cells

The human fibroblast growth factor receptor-1 primary transcript is alternatively processed to produce receptor forms that vary in their affinity for fibroblast growth factor. The inclusion of a single exon (alpha) in normal brain glial cells produces a low affinity form of the receptor. Recognition of the alpha-exon is dysregulated during neoplastic transformation of glial cells to produce a high affinity receptor form. In this study, we have identified a second intronic repressor of RNA splicing located approximately 250 nucleotides upstream of the alpha-exon. Deletion or mutation of this sequence resulted in a significant increase in exon recognition in glioblastoma cells. This intronic repressor was found to share significant sequence homology with an intronic repressor element located downstream of the alpha-exon. The two repressor elements are functionally redundant in that they are capable of inhibiting alpha-exon recognition when positioned upstream or downstream of the exon. Finally, the elements were found to mediate enhanced exclusion of an unrelated exon, but only the repressors were placed flanking the exon. However, under these conditions, the cell-specific exon exclusion was no longer maintained. These results suggest that although the alpha-exon inclusion is actively repressed in glioblastomas, the absence of trans-activators appears to be key to the production of the high affinity form of fibroblast growth factor receptor-1 in glioblastomas.