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The Scientific World Journal
Volume 2013 (2013), Article ID 703568, 8 pages
Alternative Splicing for Diseases, Cancers, Drugs, and Databases
1Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
2Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
3Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
4Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
5Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
6Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 807, Taiwan
7Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
8Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung 807, Taiwan
9Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
10Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
Received 1 April 2013; Accepted 30 April 2013
Academic Editors: F. Alvarez-Valin and A. Komiya
Copyright © 2013 Jen-Yang Tang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.
1. Introduction to Alternative Splicing
Alternative splicing of RNA is a key mechanism of increasing complexity in mRNA and proteins . Since alternative splicing apparently controls almost all human gene activities, imbalances in the this splicing process may affect the progression of various human diseases and cancers . Varying alternations in excision and/or inclusion of exons may generate different mRNA transcripts and corresponding proteins. Therefore, in addition to mediating changes in protein structure, function, and localization , alternative splicing in higher eukaryotes affects the differentiation and development of cancer and other diseases .
2. Alternative Splicing and Diseases
Alternative RNA splicing is commonly reported in neurological and muscle diseases [5–7]. Studies show that these diseases at least partly result from alternative splicing, which regulates the complexity of integral membrane proteins, including changes in their topology, solubility, and signal peptides . For example, aberrant alternative splicing has shown associations with Parkinson disease [3, 8]. For spinal muscular atrophy (SMA), the level of survival motor neuron (SMN) protein was downregulated by its alternative splicing . Therapies for SMA have recently improved by targeting RNA splicing for inclusion of exon 7 into SMN mRNA . Phorbol 12-myristate 13-acetate was reported to modulate the alternative splicing of sarcoplasmic reticulum -ATPase1 (SERCA1) which is dysregulated in myotonic dystrophy type 1 disease .
Additionally, alternative splicing reportedly regulates heart development , cardiovascular disease , blood coagulation , cholesterol homeostasis , cellular proliferation, apoptosis, immunity , and systemic sclerosis . For example, heart-specific knockout of the serine/arginine- (SR-) rich family of splicing factors, ASF/SF2, produces cardiomyopathy and affects splicing of cardiac troponin T and LIM domain-binding protein . Specific CLK inhibitors (dichloroindolyl enaminonitrile KH-CB19) of CDC2-like kinase isoforms 1 and 4 (CLK1/CLK4) can inhibit phosphorylation of cellular SR splicing factors and affect the splicing of tissue factor isoforms flTF (full-length TF) and asHTF (alternatively spliced human TF) .
Using exon array, the global mRNA splicing profile of ischemic cardiomyopathy has been investigated, and the alternative splicing of four main sarcomere genes, such as cardiac troponin T (TNNT2), cardiac troponin I (TNNI3), myosin heavy chain 7 (MYH7), and filamin C, gamma (FLNC), was dysregulated . The alternative splicing of blood coagulation-related genes including tissue factor (coagulation factor III), tissue factor pathway inhibitor (TFPI), and coagulation factor XI has been well reviewed . For cholesterol production and uptake, alternative splicing of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) and LDL receptor (LDLR) can suppress their protein activities [21, 22]. Proprotein convertase subtilisin/kexin type 9 (PCSK9) , HMG-CoA synthase (HMGCS1) , and mevalonate kinase  also reported to be involved in cholesterol biosynthesis and receptor-mediated uptake through alternative splicing.
3. Alternative Splicing and Cancer
In cancer-associated genes, splicing has important roles in oncogenesis, tumor suppression , and metastasis . Alterations in alternative splicing are commonly reported in various cancers [27–29]. Reported examples include p53 and PTEN , kallikrein-related peptidase 12 (KLK12) , breast cancer early-onset 1 (BRCA1) , protein N-arginine methyltransferases 2 (PRMT2) , and CDC25 phosphatases  in breast cancer; lysyl oxidase-like 4 (LOXL4)  and growth factor receptor-bound protein 7 (GRB7) in ovarian cancer ; androgen receptor in prostate cancer ; tissue inhibitor of metalloproteinases-1 (TIMP1) and the cell adhesion molecule CD44 in colon cancer [38, 39]; Bcl-xL, CD44, and others in lung cancer ; calpain 3 in melanoma ; and Krüppel-like factor 6 (KLF6) in liver cancer . Therefore, alternative spliced variants are potential biomarkers [43, 44] for the cancer diagnosis/prognosis and may be the targets for cancer therapy based on specific splicing correction treatments.
Single nucleotide polymorphisms (SNPs) affecting exon skipping has reviewed to confer to complex diseases . The improvement of high-throughput technologies such as RNA-Seq [46, 47] and exon arrays [48, 49] is helpful to identify the genome-wide cancer-associated splicing variants. Splicing changes may associate with lung and prostate cancer risk in terms of some SNPs. For example, a coding synonymous SNP G870A of cyclin D1 (CCND1) with a modulating ability to its splice pattern was reported to be associated with lung cancer susceptibility . Similarly, some coding synonymous SNPs may generate new splicing sites in the middle of an exon of p53 gene to change splicing . Mutations in the adenomatous polyposis coli (APC)  and BRCA1 [53, 54] genes have reported to skip exon by altering splicing. Furthermore, an intronic SNP, IVS −27 GA/IVSA, creates a new splicing factor SR-binding site and deletes two other overlapping SR-binding sites, generating three alternative splicing forms of KLF6 (KLF6 SV1-3) . This SNP was found to be associated with prostate cancer . For lung cancer study, the tumor patients with overexpression of KLF6 SV1 have lower survival [56, 57].
Actually, the information of many SNPs located in 3′ and 5′ splicing sites is searchable in the dbSNP in NCBI website (http://www.ncbi.nlm.nih.gov/snp) when the “limit” function is chosen. Researchers may choose the SNPs of splicing sites located in interested genes to identify their association relationships to diseases and cancers. A database consisting of genome-wide SNP and splicing sites, namely, ssSNPTarget  was designed to search the splice site SNPs (ssSNPs) by input of gene symbol, SNP rs number, transcript ID, or genomic position (http://variome.kobic.re.kr/ssSNPTarget/).
4. Alternative Splicing-Related Drugs and Natural Products
Splice modulating therapies have been developed for human disease [59–61] and cancer therapy [62, 63]. Antitumor drugs have been developed to target alternative splicing , splice variants , and spliceosomes [66, 67]. For example, pharmacological interventions may be affected by mRNA transcript diversity . To correct aberrant splicing, specific mRNA transcripts have been targeted in genetic disorders such as Duchenne muscular dystrophy. Since mutations of splicing factor 3B subunit 1 (SF3B1) are common in several haematological malignancies, the use of various natural products and their synthetic derivatives in therapies targeting SF3B has proven highly effective .
For drug discovery for SMA, several small molecules including sodium vanadate , aclarubicin , and indoprofen , hydroxyurea , valproate , 5-(N-ethyl-N-isopropyl)-amiloride (EIPA) , and phenylbutyrate  that increases inclusion of exon 7 of SMN2 gene have been identified, although some of them may have side effects. Recently, novel phosphatase modulators, namely, pseudocantharidins have been discovered with the similar regulating function to SMN splicing . Valproic acid was found to enhance SMN2 expression in SMA cell model involving the SF2/ASF and hnRNPA1 .
Clinical drugs such as novantrone (mitoxantrone) can enhance the effectiveness of therapeutic treatments for familial neurodegenerative diseases by stabilizing the tau pre-mRNA splicing regulatory element . Tamoxifen has proven effective for clinical treatment of estrogen receptor- (ER-) positive breast cancer . In endometrial cancer cells, alternative splicing of ER involving ER-alpha36 is also known to enhance the agonist activity of tamoxifen .
Natural products, including many xenobiotics, are also known to impair alternative splicing . For example, natural products such as pladienolide B and FR901464 [82, 83] are known to affect spliceosome function. However, the synthesis of these compounds is complicated by their multiple stereocenters. A recent study synthesized Sudemycins, which are novel analogues of FR901464. By inducing alternative gene splicing, the Sudemycins conferred both in vitro and in vivo antitumor effects . Alternative splicing has also shown regulating effects on the antitumor drug Spliceostatin A, a stabilized derivative of a Pseudomonas bacterial fermentation product  which specifically targets the SF3b spliceosome subcomplex to inhibit pre-mRNA splicing . Meayamycin, an analogue of the natural antitumor product FR901464 , inhibits RNA splicing against multidrug-resistant cells and performs antiproliferative effect against human breast cancer MCF-7 cells by suppression of alternative splicing . These results suggest that, because of their modulating effects on RNA splicing, xenobiotic analogs have potential use as chemical probes and as anticancer agents. Similarly, the polyketide natural product borrelidin inhibits cancer metastasis by modulating alternative splicing in VEGF . Antitumor effects involving alternative splicing [90, 91] have also been reported in natural dietary products. For example, resveratrol can modulate exon inclusion of SRp20 and SMN2 pre-mRNAs and induce the expression of processing factors of alternative splicing such as ASF/SF2, hnRNPA1, and HuR .
Recent studies have investigated the role of splice variants in apoptotic pathways [93, 94]. Regulation of alternative splicing genes may have anticancer effects. For example, BCL-Xs and BCL-XL have been associated with proapoptotic and antiapoptotic effects, respectively, during the progression of cancer [67, 95, 96]. The ratio of BCL-Xs/BCL-XL can be decreased by the treatment of protein kinase C (PKC) inhibitor and apoptotic inducer staurosporine in 293 cells . Soluble and membrane-bound forms of TNF receptor superfamily, member 6 (FAS) containing exons 5/7 and 5/6/7 also display proapoptotic and antiapoptotic effects, respectively . The caspase 9 (CASP9) gene has two antagonistic isoforms, proapoptotic Casp9a and prosurvival Casp9b, and its splicing is dysregulated in NSCLC lung cancer cell lines .
Alternative splicing is regulated by chromatin structure and histone modifications . In thyroid tumor cells, for example, histone deacetylase inhibitors such as butyrate modulate transcription and alternative splicing of prohibitin . A study of bovine epithelial cells showed that butyrate, a major metabolite generated by bacterial fermentation of dietary fiber in colon cells, has regulating effects on apoptosis and cell proliferation through alternative splicing . Since histone deacetylase inhibitor may have antitumor effects, the identification of this kind of inhibitor in natural products can improve drug development for tumor therapy.
5. Alternative Splicing-Related Bioinformatics Resources
Several bioinformatics analyses for the detection and regulation of alternative splicing have been well reviewed [101–103]. However, these literatures mainly focused on the methodology for detection of alternative splicing, and the databases of alternative splicing are less addressed and summarized. Here, we collect several helpful bioinformatics resources related to alternative splicing as shown in Table 1.
For example, AsMamDB  is one of the early established alternative splice databases of mammals, although their websites are not functional currently. PALS db  provides the putative alternative splicing database based on UniGene clusters of human and mouse sources which mainly consist of EST data. Similarly, some databases such as EASED  and AVATAR  are constructed by datasets of EST and mRNAs. ASAP  provides the detail annotation for exon-intron boundary, alternative splicing, and its tissue specificity for the user to design probes for distinguishing different splicing isoforms. MAASE  is also specifically designed to apply in splicing microarray experiments. In contrast, Splicy  provide the web-based tool to predict possible alternative splicing events from Affymetrix probe set inputs. ASTALAVISTA  provides alternative splicing prediction for transcriptome data from GENCODE, REFSEQ, and ENSEMBL as well as from custom gene datasets. Furthermore, SpliceCenter  is a web server for predicting the influence of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based data.
Both PolyA_DB  and AltTrans provide the information for alternative polyadenylation . For AltTrans, the AltSplice pipeline on splicing and the AltPAS pipeline on polyadenylation were implemented. ASTD  also provides the variants for splicing, transcription initiation, and polyadenylation. Of note, the dataset of transcriptomics for alternative splicing is larger than for alternative polyadenylation. GRSDB  is a mammalian database of alternative splicing based on quadruplex forming G-rich sequences which modulate the 3′ end processing of pre-mRNAs.
Additionally, several comprehensive databases for alternative splicing have been developed such as HOLLYWOOD , ASD , BIPASS , ECgene , ASPicDB , AspAlt , H-DBAS , SPLOOCE , and APPRIS . For example, the ECgene provides EST and serial analysis of gene expression (SAGE) data-based annotation and visualization for alternative splicing (AS). The ASPicDB provides EST-based tissue-specific splicing information of normal and cancer cells. The H-DBAS provides alternative splicing annotation based on RNA-Seq transcriptomics data. The APPRIS provides the annotation for principal isoform as the standard reference sequence for each gene.
Some resources of alternative splicing have special features such as splice signals in EuSplice , tandem splice sites in TassDB2 , mutational evidence-based analysis in Alternative Splicing Mutation Database , splicing proteins in SpliceAid 2 , and transcription factors in TFClass . However, the impacts of alternative splicing on the spliced transcripts encoded protein structure are less addressed. Some databases such as ProSAS  and SpliVaP  also provide the protein isoforms from the alternative splicing effects. In ProSAS, the protein isoforms of splicing transcripts are annotated in Ensembl or SwissProt. In SpliVap, protein signatures of alternative forms are annotated in terms of Pfam domains and PRINTS fingerprints.
Accumulating evidence shows that alternative splicing can be selectively targeted in several genes of cancer cells. An exciting possibility raised by this study is that the effectiveness of anticancer therapies may be enhanced by clinical drugs, natural products, and their synthesized analogs that target alternative splicing machinery. Some alternative splicing-related databases and web servers may also helpful to improve the alternative splicing therapy for treating cancer and other diseases.
This study was supported by Grants from the National Science Council (NSC101-2320-B-037-049), the Department of Health, Executive Yuan, China (DOH102-TD-C-111-002), the Technology Development Programs, Ministry of Economic Affairs, Taiwan (102-EC-17-A-01-04-0525), the Kaohsiung Medical University Research Foundation (KMUER001), and the National Sun Yat-Sen University-KMU Joint Research Project (no. NSYSU-KMU 102-034).
- D. Brett, H. Pospisil, J. Valcárcel, J. Reich, and P. Bork, “Alternative splicing and genome complexity,” Nature Genetics, vol. 30, no. 1, pp. 29–30, 2002.
- C. Ghigna, M. De Toledo, S. Bonomi et al., “Pro-metastatic splicing of Ron proto-oncogene mRNA can be reversed: therapeutic potential of bifunctional oligonucleotides and indole derivatives,” RNA Biology, vol. 7, no. 4, pp. 495–503, 2010.
- K. F. Mittendorf, C. L. Deatherage, M. D. Ohi, and C. R. Sanders, “Tailoring of membrane proteins by alternative splicing of pre-mRNA,” Biochemistry, vol. 51, no. 28, pp. 5541–5556, 2012.
- R. F. Luco, M. Allo, I. E. Schor, A. R. Kornblihtt, and T. Misteli, “Epigenetics in alternative pre-mRNA splicing,” Cell, vol. 144, no. 1, pp. 16–26, 2011.
- M. G. Poulos, R. Batra, K. Charizanis, and M. S. Swanson, “Developments in RNA splicing and disease,” Cold Spring Harbor Perspectives in Biology, vol. 3, no. 1, Article ID a000778, 2011.
- J. D. Mills and M. Janitz, “Alternative splicing of mRNA in the molecular pathology of neurodegenerative diseases,” Neurobiology of Aging, vol. 33, no. 5, pp. 1011–1024, 2012.
- K. Yap and E. V. Makeyev, “Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms,” Molecular and Cellular Neuroscience, 2013.
- R. H. Fu, S. P. Liu, S. J. Huang et al., “Aberrant alternative splicing events in Parkinson's disease,” Cell Transplantation, vol. 22, no. 4, pp. 653–661, 2013.
- J. Pearn, “Classification of spinal muscular atrophies,” Lancet, vol. 1, no. 8174, pp. 919–922, 1980.
- J. Zhou, X. Zheng, and H. Shen, “Targeting RNA-splicing for SMA treatment,” Molecules and Cells, vol. 33, no. 3, pp. 223–228, 2012.
- Y. Zhao, M. Koebis, S. Suo, S. Ohno, and S. Ishiura, “Regulation of the alternative splicing of sarcoplasmic reticulum Ca2+-ATPase1 (SERCA1) by phorbol 12-myristate 13-acetate (PMA) via a PKC pathway,” Biochemical and Biophysical Research Communications, vol. 423, no. 2, pp. 212–217, 2012.
- T. A. Cooper, “Alternative splicing regulation impacts heart development,” Cell, vol. 120, no. 1, pp. 1–2, 2005.
- E. Lara-Pezzi, A. Dopazo, and M. Manzanares, “Understanding cardiovascular disease: a journey through the genome (and what we found there),” Disease Models & Mechanisms, vol. 5, no. 4, pp. 434–443, 2012.
- V. Y. Bogdanov, “Blood coagulation and alternative pre-mRNA splicing: an overview,” Current Molecular Medicine, vol. 6, no. 8, pp. 859–869, 2006.
- M. W. Medina and R. M. Krauss, “Alternative splicing in the regulation of cholesterol homeostasis,” Current Opinion in Lipidology, vol. 24, no. 2, pp. 147–152, 2013.
- K. Endo-Umeda, S. Uno, K. Fujimori et al., “Differential expression and function of alternative splicing variants of human liver X receptor alpha,” Molecular Pharmacology, vol. 81, no. 6, pp. 800–810, 2012.
- M. Manetti, S. Guiducci, L. Ibba-Manneschi, and M. Matucci-Cerinic, “Impaired angiogenesis in systemic sclerosis: the emerging role of the antiangiogenic VEGF(165)b splice variant,” Trends in Cardiovascular Medicine, vol. 21, no. 7, pp. 204–210, 2011.
- X. Xu, D. Yang, J. H. Ding et al., “ASF/SF2-regulated CaMKIIδ alternative splicing temporally reprograms excitation-contraction coupling in cardiac muscle,” Cell, vol. 120, no. 1, pp. 59–72, 2005.
- O. Fedorov, K. Huber, A. Eisenreich et al., “Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing,” Chemistry & Biology, vol. 18, no. 1, pp. 67–76, 2011.
- S. W. Kong, Y. W. Hu, J. W. K. Ho et al., “Heart failure-associated changes in RNA splicing of sarcomere genes,” Circulation, vol. 3, no. 2, pp. 138–146, 2010.
- R. Burkhardt, E. E. Kenny, J. K. Lowe et al., “Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13,” Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 28, no. 11, pp. 2078–2084, 2008.
- H. Zhu, H. M. Tucker, K. E. Grear et al., “A common polymorphism decreases low-density lipoprotein receptor exon 12 splicing efficiency and associates with increased cholesterol,” Human Molecular Genetics, vol. 16, no. 14, pp. 1765–1772, 2007.
- R. J. Schmidt, Y. Zhang, Y. Zhao et al., “A novel splicing variant of proprotein convertase subtilisin/kexin type 9,” DNA and Cell Biology, vol. 27, no. 4, pp. 183–189, 2008.
- G. Gil, J. R. Smith, J. L. Goldstein, and M. S. Brown, “Optional exon in the 5′-untranslated region of 3-hydroxy-3-methylglutaryl coenzyme A synthase gene: conserved sequence and splicing pattern in humans and hamsters,” Proceedings of the National Academy of Sciences of the United States of America, vol. 84, no. 7, pp. 1863–1866, 1987.
- S. M. Houten, J. Koster, G. J. Romeijn et al., “Organization of the mevalonate kinase (MVK) gene and identification of novel mutations causing mevalonic aciduria and hyperimmunoglobulinaemia D and periodic fever syndrome,” European Journal of Human Genetics, vol. 9, no. 4, pp. 253–259, 2001.
- D. Kaida, T. Schneider-Poetsch, and M. Yoshida, “Splicing in oncogenesis and tumor suppression,” Cancer Science, vol. 103, no. 9, pp. 1611–1616, 2012.
- R. M. Hagen and M. R. Ladomery, “Role of splice variants in the metastatic progression of prostate cancer,” Biochemical Society Transactions, vol. 40, no. 4, pp. 870–874, 2012.
- J. Sampath and L. M. Pelus, “Alternative splice variants of survivin as potential targets in cancer,” Current Drug Discovery Technologies, vol. 4, no. 3, pp. 174–191, 2007.
- K. Miura, W. Fujibuchi, and I. Sasaki, “Alternative pre-mRNA splicing in digestive tract malignancy,” Cancer Science, vol. 102, no. 2, pp. 309–316, 2011.
- N. Okumura, H. Yoshida, Y. Kitagishi, Y. Nishimura, and S. Matsuda, “Alternative splicings on p53, BRCA1 and PTEN genes involved in breast cancer,” Biochemical and Biophysical Research Communications, vol. 413, no. 3, pp. 395–399, 2011.
- M. Talieri, M. Devetzi, A. Scorilas et al., “Human kallikrein-related peptidase 12 (KLK12) splice variants expression in breast cancer and their clinical impact,” Tumor Biology, vol. 33, no. 4, pp. 1075–1084, 2012.
- C. Tammaro, M. Raponi, D. I. Wilson, and D. Baralle, “BRCA1 exon 11 alternative splicing, multiple functions and the association with cancer,” Biochemical Society Transactions, vol. 40, no. 4, pp. 768–772, 2012.
- J. Zhong, R. X. Cao, X. Y. Zu et al., “Identification and characterization of novel spliced variants of PRMT2 in breast carcinoma,” FEBS Journal, vol. 279, no. 2, pp. 316–335, 2012.
- H. Albert, S. Santos, E. Battaglia, M. Brito, C. Monteiro, and D. Bagrel, “Differential expression of CDC25 phosphatases splice variants in human breast cancer cells,” Clinical Chemistry and Laboratory Medicine, vol. 49, no. 10, pp. 1707–1714, 2011.
- S. Sebban, R. Golan-Gerstl, R. Karni, O. Vaksman, B. Davidson, and R. Reich, “Alternatively spliced lysyl oxidase-like 4 isoforms have a pro-metastatic role in cancer,” Clinical and Experimental Metastasis, vol. 30, no. 1, pp. 103–117, 2013.
- Y. Wang, D. W. Chan, V. W. S. Liu, P. M. Chiu, and H. Y. S. Ngan, “Differential functions of growth factor receptor-bound protein 7 (GRB7) and its variant GRB7v in ovarian carcinogenesis,” Clinical Cancer Research, vol. 16, no. 9, pp. 2529–2539, 2010.
- S. Haile and M. D. Sadar, “Androgen receptor and its splice variants in prostate cancer,” Cellular and Molecular Life Sciences, vol. 68, no. 24, pp. 3971–3981, 2011.
- P. A. Usher, A. M. Sieuwerts, A. Bartels et al., “Identification of alternatively spliced TIMP-1 mRNA in cancer cell lines and colon cancer tissue,” Molecular Oncology, vol. 1, no. 2, pp. 205–215, 2007.
- D. C. Gotley, J. Fawcett, M. D. Walsh, J. A. Reeder, D. L. Simmons, and T. M. Antalis, “Alternatively spliced variants of the cell adhesion molecule CD44 and tumour progression in colorectal cancer,” British Journal of Cancer, vol. 74, no. 3, pp. 342–351, 1996.
- R. Pio and L. M. Montuenga, “Alternative splicing in lung cancer,” Journal of Thoracic Oncology, vol. 4, no. 6, pp. 674–678, 2009.
- D. Moretti, B. Del Bello, E. Cosci, M. Biagioli, C. Miracco, and E. Maellaro, “Novel variants of muscle calpain 3 identified in human melanoma cells: cisplatin-induced changes in vitro and differential expression in melanocytic lesions,” Carcinogenesis, vol. 30, no. 6, pp. 960–967, 2009.
- N. Hanoun, C. Bureau, T. Diab et al., “The SV2 variant of KLF6 is down-regulated in hepatocellular carcinoma and displays anti-proliferative and pro-apoptotic functions,” Journal of Hepatology, vol. 53, no. 5, pp. 880–888, 2010.
- Q. Yi and L. Tang, “Alternative spliced variants as biomarkers of colorectal cancer,” Current Drug Metabolism, vol. 12, no. 10, pp. 966–974, 2011.
- G. S. Omenn, A. K. Yocum, and R. Menon, “Alternative splice variants, a new class of protein cancer biomarker candidates: findings in pancreatic cancer and breast cancer with systems biology implications,” Disease Markers, vol. 28, no. 4, pp. 241–251, 2010.
- Y. Lee, E. R. Gamazon, E. Rebman et al., “Variants affecting exon skipping contribute to complex traits,” PLOS Genetics, vol. 8, no. 10, Article ID e1002998, 2012.
- H. Feng, Z. Qin, and X. Zhang, “Opportunities and methods for studying alternative splicing in cancer with RNA-Seq,” Cancer Letters, 2012.
- G. Li, J. H. Bahn, J. H. Lee et al., “Identification of allele-specific alternative mRNA processing via transcriptome sequencing,” Nucleic Acids Research, vol. 40, no. 13, article e104, 2012.
- L. Xi, A. Feber, V. Gupta et al., “Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer,” Nucleic Acids Research, vol. 36, no. 20, pp. 6535–6547, 2008.
- C. Ben-Dov, B. Hartmann, J. Lundgren, and J. Valcárcel, “Genome-wide analysis of alternative pre-mRNA splicing,” Journal of Biological Chemistry, vol. 283, no. 3, pp. 1229–1233, 2008.
- O. Gautschi, D. Ratschiller, M. Gugger, D. C. Betticher, and J. Heighway, “Cyclin D1 in non-small cell lung cancer: a key driver of malignant transformation,” Lung Cancer, vol. 55, no. 1, pp. 1–14, 2007.
- G. Lamolle, M. Marin, and F. Alvarez-Valin, “Silent mutations in the gene encoding the p53 protein are preferentially located in conserved amino acid positions and splicing enhancers,” Mutation Research, vol. 600, no. 1-2, pp. 102–112, 2006.
- D. W. Neklason, C. H. Solomon, A. L. Dalton, S. K. Kuwada, and R. W. Burt, “Intron 4 mutation in APC gene results in splice defect and attenuated FAP phenotype,” Familial Cancer, vol. 3, no. 1, pp. 35–40, 2004.
- M. Raponi, J. Kralovicova, E. Copson et al., “Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6,” Human Mutation, vol. 32, no. 4, pp. 436–444, 2011.
- H. X. Liu, L. Cartegni, M. Q. Zhang, and A. R. Krainer, “A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes,” Nature Genetics, vol. 27, no. 1, pp. 55–58, 2001.
- G. Narla, A. DiFeo, H. L. Reeves et al., “A germline DNA polymorphism enhances alternative splicing of the KLF6 tumor suppressor gene and is associated with increased prostate cancer risk,” Cancer Research, vol. 65, no. 4, pp. 1213–1222, 2005.
- G. Narla, A. Difeo, S. Yao et al., “Targeted inhibition of the KLF6 splice variant, KLF6 SV1, suppresses prostate cancer cell growth and spread,” Cancer Research, vol. 65, no. 13, pp. 5761–5768, 2005.
- A. DiFeo, L. Feld, E. Rodriguez et al., “A functional role for KLF6-SV1 in lung adenocarcinoma prognosis and chemotherapy response,” Cancer Research, vol. 68, no. 4, pp. 965–970, 2008.
- J. O. Yang, W. Y. Kim, and J. Bhak, “ssSNPTarget: genome-wide splice-site single nucleotide polymorphism database,” Human Mutation, vol. 30, no. 12, pp. E1010–E1020, 2009.
- A. G. Douglas and M. J. Wood, “RNA splicing: disease and therapy,” Briefings in Functional Genomics, vol. 10, no. 3, pp. 151–164, 2011.
- R. K. Singh and T. A. Cooper, “Pre-mRNA splicing in disease and therapeutics,” Trends in Molecular Medicine, vol. 18, no. 8, pp. 472–482, 2012.
- P. Spitali and A. Aartsma-Rus, “Splice modulating therapies for human disease,” Cell, vol. 148, no. 6, pp. 1085–1088, 2012.
- K. Miura, W. Fujibuchi, and M. Unno, “Splice isoforms as therapeutic targets for colorectal cancer,” Carcinogenesis, vol. 33, no. 12, pp. 2311–2319, 2012.
- J. P. Maciejewski and R. A. Padgett, “Defects in spliceosomal machinery: a new pathway of leukaemogenesis,” British Journal of Haematology, vol. 158, no. 2, pp. 165–173, 2012.
- M. Hagiwara, “Alternative splicing: a new drug target of the post-genome era,” Biochimica et Biophysica Acta, vol. 1754, no. 1-2, pp. 324–331, 2005.
- C. A. Blair and X. Zi, “Potential molecular targeting of splice variants for cancer treatment,” Indian Journal of Experimental Biology, vol. 49, no. 11, pp. 836–839, 2011.
- R. J. Van Alphen, E. A. C. Wiemer, H. Burger, and F. A. L. M. Eskens, “The spliceosome as target for anticancer treatment,” British Journal of Cancer, vol. 100, no. 2, pp. 228–232, 2009.
- S. Bonnal, L. Vigevani, and J. Valcarcel, “The spliceosome as a target of novel antitumour drugs,” Nature Reviews Drug Discovery, vol. 11, no. 11, pp. 847–859, 2012.
- E. S. Barrie, R. M. Smith, J. C. Sanford, and W. Sadee, “mRNA transcript diversity creates new opportunities for pharmacological intervention,” Molecular Pharmacology, vol. 81, no. 5, pp. 620–630, 2012.
- M. L. Zhang, C. L. Lorson, E. J. Androphy, and J. Zhou, “An in vivo reporter system for measuring increased inclusion of exon 7 in SMN2 mRNA: potential therapy of SMA,” Gene Therapy, vol. 8, no. 20, pp. 1532–1538, 2001.
- C. Andreassi, J. Jarecki, J. Zhou et al., “Aclarubicin treatment restores SMN levels to cells derived from type I spinal muscular atrophy patients,” Human Molecular Genetics, vol. 10, no. 24, pp. 2841–2849, 2001.
- M. R. Lunn, D. E. Root, A. M. Martino et al., “Indoprofen upregulates the survival motor neuron protein through a cyclooxygenase-independent mechanism,” Chemistry and Biology, vol. 11, no. 11, pp. 1489–1493, 2004.
- C. Xu, X. Chen, S. M. Grzeschik, M. Ganta, and C. H. Wang, “Hydroxyurea enhances SMN2 gene expression through nitric oxide release,” Neurogenetics, vol. 12, no. 1, pp. 19–24, 2011.
- C. C. Weihl, A. M. Connolly, and A. Pestronk, “Valproate may improve strength and function in patients with type III/IV spinal muscle atrophy,” Neurology, vol. 67, no. 3, pp. 500–501, 2006.
- C. Y. Yuo, H. H. Lin, Y. S. Chang, W. K. Yang, and J. G. Chang, “5-(N-ethyl-N-isopropyl)-amiloride enhances SMN2 exon 7 inclusion and protein expression in spinal muscular atrophy cells,” Annals of Neurology, vol. 63, no. 1, pp. 26–34, 2008.
- C. Andreassi, C. Angelozzi, F. D. Tiziano et al., “Phenylbutyrate increases SMN expression in vitro: relevance for treatment of spinal muscular atrophy,” European Journal of Human Genetics, vol. 12, no. 1, pp. 59–65, 2004.
- Z. Zhang, O. Kelemen, M. A. Van Santen et al., “Synthesis and characterization of pseudocantharidins, novel phosphatase modulators that promote the inclusion of exon 7 into the SMN (survival of motoneuron) pre-mRNA,” Journal of Biological Chemistry, vol. 286, no. 12, pp. 10126–10136, 2011.
- I. S. K. Harahap, T. Saito, L. P. San et al., “Valproic acid increases SMN2 expression and modulates SF2/ASF and hnRNPA1 expression in SMA fibroblast cell lines,” Brain and Development, 2011.
- S. Zheng, Y. Chen, C. P. Donahue, M. S. Wolfe, and G. Varani, “Structural Basis for Stabilization of the Tau Pre-mRNA Splicing Regulatory Element by Novantrone (Mitoxantrone),” Chemistry and Biology, vol. 16, no. 5, pp. 557–566, 2009.
- J. S. Lewis and V. C. Jordan, “Selective estrogen receptor modulators (SERMs): mechanisms of anticarcinogenesis and drug resistance,” Mutation Research, vol. 591, no. 1-2, pp. 247–263, 2005.
- S. L. Lin, L. Y. Yan, X. T. Zhang et al., “ER-α36, a variant of ER-α, promotes tamoxifen agonist action in endometrial cancer cells via the MAPK/ERK and PI3K/Akt pathways,” PLoS ONE, vol. 5, no. 2, Article ID e9013, 2010.
- E. Zaharieva, J. K. Chipman, and M. Soller, “Alternative splicing interference by xenobiotics,” Toxicology, vol. 296, pp. 1–12, 2012.
- D. Kaida, H. Motoyoshi, E. Tashiro et al., “Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA,” Nature Chemical Biology, vol. 3, no. 9, pp. 576–583, 2007.
- Y. Kotake, K. Sagane, T. Owa et al., “Splicing factor SF3b as a target of the antitumor natural product pladienolide,” Nature Chemical Biology, vol. 3, no. 9, pp. 570–575, 2007.
- L. Fan, C. Lagisetti, C. C. Edwards, T. R. Webb, and P. M. Potter, “Sudemycins, novel small molecule analogues of FR901464, induce alternative gene splicing,” ACS Chemical Biology, vol. 6, no. 6, pp. 582–589, 2011.
- A. Corrionero, B. Miñana, and J. Valcárcel, “Reduced fidelity of branch point recognition and alternative splicing induced by the anti-tumor drug spliceostatin A,” Genes and Development, vol. 25, no. 5, pp. 445–459, 2011.
- R. Furumai, K. Uchida, Y. Komi et al., “Spliceostatin A blocks angiogenesis by inhibiting global gene expression including VEGF,” Cancer Science, vol. 101, no. 11, pp. 2483–2489, 2010.
- H. Nakajima, B. Sato, T. Fujita, S. Takase, H. Terano, and M. Okuhara, “New antitumor substances, FR901463, FR901464 and FR901465: I. Taxonomy, fermentation, isolation, physico-chemical properties and biological activities,” Journal of Antibiotics, vol. 49, no. 12, pp. 1196–1203, 1996.
- B. J. Albert, P. A. McPherson, K. O'Brien et al., “Meayamycin inhibits pre-messenger RNA splicing and exhibits picomolar activity against multidrug-resistant cells,” Molecular Cancer Therapeutics, vol. 8, no. 8, pp. 2308–2318, 2009.
- J. Woolard, W. Vousden, S. J. Moss et al., “Borrelidin modulates the alternative splicing of VEGF in favour of anti-angiogenic isoforms,” Chemical Science, vol. 2011, no. 2, pp. 273–278, 2011.
- U. Shamim, S. Hanif, A. Albanyan et al., “Resveratrol-induced apoptosis is enhanced in low pH environments associated with cancer,” Journal of Cellular Physiology, vol. 227, no. 4, pp. 1493–1500, 2012.
- J. Jakubikova, D. Cervi, M. Ooi et al., “Anti-tumor activity and signaling events triggered by the isothiocyanates, sulforaphane and phenethyl isothiocyanate, in multiple myeloma,” Haematologica, vol. 96, no. 8, pp. 1170–1179, 2011.
- M. A. Markus, F. Z. Marques, and B. J. Morris, “Resveratrol, by modulating RNA processing factor levels, can influence the alternative splicing of pre-mRNAs,” PLoS One, vol. 6, no. 12, Article ID e28926, 2011.
- K. Miura, W. Fujibuchi, and M. Unno, “Splice variants in apoptotic pathway,” Experimental Oncology, vol. 34, no. 3, pp. 212–217, 2012.
- C. Schwerk and K. Schulze-Osthoff, “Regulation of apoptosis by alternative pre-mRNA splicing,” Molecular Cell, vol. 19, no. 1, pp. 1–13, 2005.
- L. Shkreta, U. Froehlich, E. R. Paquet, J. Toutant, S. A. Elela, and B. Chabot, “Anticancer drugs affect the alternative splicing of Bcl-x and other human apoptotic genes,” Molecular Cancer Therapeutics, vol. 7, no. 6, pp. 1398–1409, 2008.
- J. Lee, J. Zhou, X. Zheng et al., “Identification of a novel cis-element that regulates alternative splicing of Bcl-x pre-mRNA,” Biochemical and Biophysical Research Communications, vol. 420, no. 2, pp. 467–472, 2012.
- T. Revil, J. Toutant, L. Shkreta, D. Garneau, P. Cloutier, and B. Chabot, “Protein kinase C-dependent control of Bcl-x alternative splicing,” Molecular and Cellular Biology, vol. 27, no. 24, pp. 8431–8441, 2007.
- J. C. Shultz, R. W. Goehe, D. S. Wijesinghe et al., “Alternative splicing of caspase 9 is modulated by the phosphoinositide 3-kinase/Akt pathway via phosphorylation of SRp30a,” Cancer Research, vol. 70, no. 22, pp. 9185–9196, 2010.
- C. Puppin, N. Passon, A. Franzoni, D. Russo, and G. Damante, “Histone deacetylase inhibitors control the transcription and alternative splicing of prohibitin in thyroid tumor cells,” Oncology Reports, vol. 25, no. 2, pp. 393–397, 2011.
- S. Wu, C. Li, W. Huang, W. Li, and R. W. Li, “Alternative splicing regulated by butyrate in bovine epithelial cells,” PLoS One, vol. 7, no. 6, Article ID e39182, 2012.
- C. Lee and Q. Wang, “Bioinformatics analysis of alternative splicing,” Briefings in Bioinformatics, vol. 6, no. 1, pp. 23–33, 2005.
- L. D. Florea, “Bioinformatics of alternative splicing and its regulation,” Briefings in Bioinformatics, vol. 7, no. 1, pp. 55–69, 2006.
- N. Kim and C. Lee, “Bioinformatics detection of alternative splicing,” Methods in Molecular Biology, vol. 452, pp. 179–197, 2008.
- H. Ji, Q. Zhou, F. Wen, H. Xia, X. Lu, and Y. Li, “AsMamDB: an alternative splice database of mammals,” Nucleic Acids Research, vol. 29, no. 1, pp. 260–263, 2001.
- Y. H. Huang, Y. T. Chen, J. J. Lai, S. T. Yang, and U. C. Yang, “PALS db: putative alternative splicing database,” Nucleic Acids Research, vol. 30, no. 1, pp. 186–190, 2002.
- C. Lee, L. Atanelov, B. Modrek, and Y. Xing, “ASAP: the alternative splicing annotation project,” Nucleic Acids Research, vol. 31, no. 1, pp. 101–105, 2003.
- H. Pospisil, A. Herrmann, R. H. Bortfeldt, and J. G. Reich, “EASED: Extended Alternatively Spliced EST Database,” Nucleic Acids Research, vol. 32, pp. D70–D74, 2004.
- F. R. Hsu, H. Y. Chang, Y. L. Lin et al., “AVATAR: a database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs,” , Bioinformation, vol. 1, no. 1, pp. 16–18, 2005.
- C. L. Zheng, Y. S. Kwon, L. I. Hai-Ri et al., “MAASE: an alternative splicing database designed for supporting splicing microarray applications,” RNA, vol. 11, no. 12, pp. 1767–1776, 2005.
- H. Zhang, J. Hu, M. Recce, and B. Tian, “PolyA_DB: a database for mammalian mRNA polyadenylation,” Nucleic Acids Research, vol. 33, pp. D116–D120, 2005.
- V. Le Texier, J. J. Riethoven, V. Kumanduri et al., “AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation,” BMC Bioinformatics, vol. 7, article 169, 2006.
- R. Kostadinov, N. Malhotra, M. Viotti, R. Shine, L. D'Antonio, and P. Bagga, “GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences,” Nucleic Acids Research, vol. 34, pp. D119–124, 2006.
- D. Holste, G. Huo, V. Tung, and C. B. Burge, “HOLLYWOOD: a comparative relational database of alternative splicing,” Nucleic Acids Research, vol. 34, pp. D56–62, 2006.
- S. Stamm, J. J. Riethoven, V. Le Texier et al., “ASD: a bioinformatics resource on alternative splicing,” Nucleic Acids Research, vol. 34, pp. D46–55, 2006.
- D. Rambaldi, B. Felice, V. Praz, P. Bucher, D. Cittaro, and A. Guffanti, “Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data,” BMC Bioinformatics, vol. 8, no. 1, article no. S17, 2007.
- S. Foissac and M. Sammeth, “ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets,” Nucleic Acids Research, vol. 35, pp. W297–299, 2007.
- Z. Lacroix, C. Legendre, L. Raschid, and B. Snyder, “BIPASS: BioInformatics Pipeline Alternative Splicing Services,” Nucleic Acids Research, vol. 35, pp. W292–296, 2007.
- Y. Lee, Y. Lee, B. Kim et al., “ECgene: an alternative splicing database update,” Nucleic Acids Research, vol. 35, no. 1, pp. D99–D103, 2007.
- A. Bhasi, R. V. Pandey, S. P. Utharasamy, and P. Senapathy, “EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes,” Bioinformatics, vol. 23, no. 14, pp. 1815–1823, 2007.
- M. C. Ryan, B. R. Zeeberg, N. J. Caplen et al., “SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies,” BMC Bioinformatics, vol. 9, article 313, 2008.
- T. Castrignanò, M. D'Antonio, A. Anselmo et al., “ASPicDB: a database resource for alternative splicing analysis,” Bioinformatics, vol. 24, no. 10, pp. 1300–1304, 2008.
- J. M. Bechtel, P. Rajesh, I. Ilikchyan et al., “The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence,” BMC Research Notes, vol. 1, article 3, 2008.
- F. Birzele, R. Küffner, F. Meier, F. Oefinger, C. Potthast, and R. Zimmer, “ProSAS: a database for analyzing alternative splicing in the context of protein structures,” Nucleic Acids Research, vol. 36, no. 1, pp. D63–D68, 2008.
- M. Floris, M. Orsini, and T. A. Thanaraj, “Splice-mediated variants of proteins (SpliVaP)—data and characterization of changes in signatures among protein isoforms due to alternative splicing,” BMC Genomics, vol. 9, article 453, 2008.
- A. Bhasi, P. Philip, V. T. Sreedharan, and P. Senapathy, “AspAlt: a tool for inter-database, inter-genomic and user-specific comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes,” Genomics, vol. 94, no. 1, pp. 48–54, 2009.
- G. Koscielny, V. L. Texier, C. Gopalakrishnan et al., “ASTD: the Alternative Splicing and Transcript Diversity database,” Genomics, vol. 93, no. 3, pp. 213–220, 2009.
- R. Sinha, T. Lenser, N. Jahn et al., “TassDB2: a comprehensive database of subtle alternative splicing events,” BMC Bioinformatics, vol. 11, article 216, 2010.
- J. I. Takeda, Y. Suzuki, R. Sakate et al., “H-DBAS: Human-transcriptome database for alternative splicing: update 2010,” Nucleic Acids Research, vol. 38, no. 1, Article ID gkp984, pp. D86–D90, 2009.
- J. E. Kroll, P. A. Galante, D. T. Ohara, F. C. Navarro, L. Ohno-Machado, and S. J. de Souza, “SPLOOCE: a new portal for the analysis of human splicing variants,” RNA Biology, vol. 9, no. 11, pp. 1339–1343, 2012.
- J. M. Rodriguez, P. Maietta, I. Ezkurdia et al., “APPRIS: annotation of principal and alternative splice isoforms,” Nucleic Acids Research, vol. 41, pp. 110–117, 2013.
- F. Piva, M. Giulietti, A. B. Burini, and G. Principato, “SpliceAid 2: a database of human splicing factors expression data and RNA target motifs,” Human Mutation, vol. 33, no. 1, pp. 81–85, 2012.
- E. Wingender, T. Schoeps, and J. Donitz, “TFClass: an expandable hierarchical classification of human transcription factors,” Nucleic Acids Research, vol. 41, pp. 165–170, 2013.