Wang Z, Lo HS, Yang H, Gere S, Hu Y, Buetow KH et al.. Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer. Cancer Res 63: 655-657

Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland 20877,USA.
Cancer Research (Impact Factor: 9.33). 03/2003; 63(3):655-7.
Source: PubMed


A genome-wide computational screen was performed to identify tumor-associated alternative RNA splicing isoforms. A BLAST algorithm was used to compare 11,014 genes from RefSeq with 3,471,822 human expressed sequence tag sequences. The screen identified 26,258 alternative splicing isoforms of which 845 were significantly associated with human cancer, and 54 were specifically associated with liver cancer. Furthermore, canonical GT-AG splice junctions were used significantly less frequently in the alternative splicing isoforms in tumors. Reverse transcription-PCR experiments confirmed association of the alternative splicing isoforms with tumors. These results suggest that alternative splicing may have potential as a diagnostic marker for cancer.

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    • "The most prevalent types of alternative splicing are the variable inclusion of an entire exon (cassette exon), the selection of alternative splice sites upstream of or downstream from the 3 ′ or the 5 ′ splice site, as well as intron retention (Wang et al. 2008). Defects in splicing lead to many human genetic diseases (Krawczak et al. 1992; Cartegni et al. 2002; Faustino and Cooper 2003) and splicing mutations in a number of genes involved in growth control have been implicated in multiple types of cancer (Carstens et al. 1997; Mercatante et al. 2001; Wang et al. 2003; Xu and Lee 2003; Bartel et al. 2004; Brinkman 2004). Insights into the basic mechanisms of pre-mRNA splicing and splice-site recognition are therefore fundamental to understanding regulated gene expression and human disease. "
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    ABSTRACT: Alternative splicing is a key player in the creation of complex mammalian transcriptomes and its misregulation is associated with many human diseases. Multiple mRNA isoforms are generated from most human genes, a process mediated by the interplay of various RNA signature elements and trans-acting factors that guide spliceosomal assembly and intron removal. Here, we introduce a splicing predictor that evaluates hundreds of RNA features simultaneously to successfully differentiate between exons that are constitutively spliced, exons that undergo alternative 5' or 3' splice-site selection, and alternative cassette-type exons. Surprisingly, the splicing predictor did not feature strong discriminatory contributions from binding sites for known splicing regulators. Rather, the ability of an exon to be involved in one or multiple types of alternative splicing is dictated by its immediate sequence context, mainly driven by the identity of the exon's splice sites, the conservation around them, and its exon/intron architecture. Thus, the splicing behavior of human exons can be reliably predicted based on basic RNA sequence elements. © 2015 Busch and Hertel; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
    Full-text · Article · Mar 2015 · RNA
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    • "Although AS is the major source of protein diversity in human being, it has not been extensively documented with respect to pathology, excepted for cancer [19]. We confirmed the existence of AS events, in vivo and in vitro correlated with CKD, but this level of control of gene expression is infrequent. "
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    ABSTRACT: The control of gene expression in the course of chronic kidney disease (CKD) is not well addressed. Alternative splicing is a common way to increase complexity of proteins. More than 90% of human transcripts are alternatively spliced. We hypothesised that CKD can induce modification of the alternative splicing machinery. During mutation screening in autosomal dominant polycystic kidney disease, we identified in mononuclear cells (PBMC), an alternative splicing event on the exon 30 of PKD1 gene, the gene implicated in this disease. This alternative splice variant was not correlated with the cystic disease but with CKD. To confirm the association between this variant and CKD, a monocentric clinical study was performed with 3 different groups according to their kidney function (CKD5D, CKD3-5 and normal kidney function). An exon microarray approach was used to highlight splicing events in whole human genome in a normal cell model (fibroblasts) incubated with uremic serum. Alternative splicing variants identified were confirmed by RT-PCR. The splicing variant of the exon 30 of PKD1 was more frequent in PBMCs from patients with CKD compared to control. With the microarray approach, despite the analysis of more than 230 000 probes, we identified 36 genes with an abnormal splicing index evocating splicing event in fibroblasts exposed to uremic serum. Only one abnormal splicing event in one gene, ADH1B, was confirmed by RT-PCR. We observed two alternative spliced genes in two different cell types associated with CKD. Alternative splicing could play a role in the control of gene expression during CKD but it does not seem to be a major mechanism.
    Full-text · Article · Dec 2013 · PLoS ONE
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    • "These events greatly increase the functional complexity of the human genome. Some isoforms apparently have active roles in various cell types or tissues [20,21]. Therefore, although alternative splicing is an effective mechanism for generating isoforms, the isoforms may lack functional elements in either the coding or noncoding regions of a primary transcript. "
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    ABSTRACT: MicroRNAs are very small non-coding RNAs that interact with microRNA recognition elements (MREs) on their target messenger RNAs. Varying the concentration of a given microRNA may influence the expression of many target proteins. Yet, the expression of a specific target protein can be fine-tuned by alternative cleavage and polyadenylation to the corresponding mRNA. This study showed that alternative splicing of mRNA is a fine-tuning mechanism in the cellular regulatory network. The splicing-regulated MREs are often highly repressive MREs. This phenomenon was observed not only in the hsa-miR-148a-regulated DNMT3B gene, but also in many target genes regulated by hsa-miR-124, hsa-miR-1, and hsa-miR-181a. When a gene contains multiple MREs in transcripts, such as the VEGF gene, the splicing-regulated MREs are again the highly repressive MREs. Approximately one-third of the analysable human MREs in MiRTarBase and TarBase can potentially perform the splicing-regulated fine-tuning. Interestingly, the high (+30%) repression ratios observed in most of these splicing-regulated MREs indicate associations with functions. For example, the MRE-free transcripts of many oncogenes, such as N-RAS and others may escape microRNA-mediated suppression in cancer tissues. This fine-tuning mechanism revealed associations with highly repressive MRE. Since high-repression MREs are involved in many important biological phenomena, the described association implies that splicing-regulated MREs are functional. A possible application of this observed association is in distinguishing functionally relevant MREs from predicted MREs.
    Full-text · Article · Jul 2013 · BMC Genomics
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