Differentially expressed alternatively spliced genes in Malignant Pleural Mesothelioma identified using massively parallel transcriptome sequencing

BMC Medical Genetics

Volumn 10, Issue , 2009, Pages

  Dong, Lingsheng ^a   Jensen, Roderick V ^b   De Rienzo, Assunta ^a   Gordon, Gavin J ^a   Xu, Yanlong ^a   Sugarbaker, David J ^a   Bueno, Raphael ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; RNA PRECURSOR;

ALTERNATIVE RNA SPLICING; ARTICLE; CANCER GENETICS; CONTROLLED STUDY; EXON; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC DATABASE; HUMAN; HUMAN TISSUE; LUNG PARENCHYMA; MALIGNANT MESOTHELIOMA; PLEURA MESOTHELIOMA; REAL TIME POLYMERASE CHAIN REACTION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; MESOTHELIOMA; METHODOLOGY; PLEURA TUMOR; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS;

ALTERNATIVE SPLICING; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MESOTHELIOMA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLEURAL NEOPLASMS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA PRECURSORS; SEQUENCE ANALYSIS, RNA;

EID: 74749088624     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-10-149     Document Type: Article

References (34)

1. Buratti E, Baralle M, Baralle FE. Defective splicing, disease and therapy: searching for master checkpoints in exon definition. Nucleic Acids Res 2006, 34(12):3494-3510. 10.1093/nar/gkl498, 1524908, 16855287.
2. Tanko Q, Franklin B, Lynch H, Knezetic J. A hMLH1 genomic mutation and associated novel mRNA defects in a hereditary non-polyposis colorectal cancer family. Mutat Res 2002, 503(1-2):37-42.
3. Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Gervais-Bird J, Madden R, Paquet ER, Koh C, Venables JP, Prinos P, et al. Multiple alternative splicing markers for ovarian cancer. Cancer Res 2008, 68(3):657-663. 10.1158/0008-5472.CAN-07-2580, 18245464.
4. Hoffman JD, Hallam SE, Venne VL, Lyon E, Ward K. Implications of a novel cryptic splice site in the BRCA1 gene. Am J Med Genet 1998, 80(2):140-144. 10.1002/(SICI)1096-8628(19981102)80:2<140::AID-AJMG10>3.0.CO;2-L, 9805131.
5. Honda K, Yamada T, Seike M, Hayashida Y, Idogawa M, Kondo T, Ino Y, Hirohashi S. Alternative splice variant of actinin-4 in small cell lung cancer. Oncogene 2004, 23(30):5257-5262. 10.1038/sj.onc.1207652, 15122314.
6. Venables JP. Aberrant and alternative splicing in cancer. Cancer Res 2004, 64(21):7647-7654. 10.1158/0008-5472.CAN-04-1910, 15520162.
7. Coulson JM, Edgson JL, Woll PJ, Quinn JP. A splice variant of the neuron-restrictive silencer factor repressor is expressed in small cell lung cancer: a potential role in derepression of neuroendocrine genes and a useful clinical marker. Cancer Res 2000, 60(7):1840-1844.
8. Thorsen K, Sorensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AM, Kruhoffer M, Laurberg S, Borre M, Wang K, Brunak S, Krainer AR, Torring N, Dyrskjot L, Andersen CL, Orntoft TF. Alternative splicing in colon, bladder, and prostate cancer identified by exon-array analysis. Mol Cell Proteomics 2008, 7(7):1214-24. 10.1074/mcp.M700590-MCP200, 18353764.
9. Garcia-Blanco MA. Alternative splicing: therapeutic target and tool. Prog Mol Subcell Biol 2006, 44:47-64. full_text, 17076264.
10. Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res 2001, 29(13):2850-2859. 10.1093/nar/29.13.2850, 55780, 11433032.
11. Gupta S, Zink D, Korn B, Vingron M, Haas SA. Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics 2004, 20(16):2579-2585. 10.1093/bioinformatics/bth288, 15117759.
12. Roy M, Xu Q, Lee C. Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms. Nucleic Acids Res 2005, 33(16):5026-5033. 10.1093/nar/gki792, 1201329, 16147986.
13. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003, 302(5653):2141-2144. 10.1126/science.1090100, 14684825.
14. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
15. Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, De Rienzo A, Maulik G, Glickman JN, Chirieac LR, Hartman ML, Taillon BE, et al. Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc Natl Acad Sci USA 2008, 105(9):3521-3526. 10.1073/pnas.0712399105, 2265129, 18303113.
16. Thierry-Mieg D, Thierry-Mieg J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol 2006, 7(Suppl 1):11-14.
17. Goncalves J, Edvards DJ. Use of an exon software package to identify global gene splicing and gene expression regulation. American Biotechnology Laboratory 25(4). International Scientific Communications Inc., Shelton, CT.
18. Venables WN, Riley BD. Modern Applied Statistics with S-Plus. 1997, New York: Springer.
19. Faul F, Erdfelder E, Lang AG, Buchner A. G*Power 3: a flexible statistical power analysis program for the social, behavioral, and biomedical sciences. Behav Res Methods 2007, 39(2):175-191.
20. Cowell JK, Hawthorn L. The application of microarray technology to the analysis of the cancer genome. Curr Mol Med 2007, 7(1):103-120. 10.2174/156652407779940387, 17311536.
21. Venables JP, Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Koh C, Gervais-Bird J, Lapointe E, Froehlich U, Durand M, et al. Identification of alternative splicing markers for breast cancer. Cancer Res 2008, 68(22):9525-9531. 10.1158/0008-5472.CAN-08-1769, 19010929.
22. Miwa T, Manabe Y, Kurokawa K, Kamada S, Kanda N, Bruns G, Ueyama H, Kakunaga T. Structure, chromosome location, and expression of the human smooth muscle (enteric type) gamma-actin gene: evolution of six human actin genes. Mol Cell Biol 1991, 11(6):3296-3306. 360182, 1710027.
23. Watson MB, Lind MJ, Smith L, Drew PJ, Cawkwell L. Expression microarray analysis reveals genes associated with in vitro resistance to cisplatin in a cell line model. Acta Oncol 2007, 46(5):651-658. 10.1080/02841860601156157, 17562441.
24. Li GY, Kim M, Kim JH, Lee MO, Chung JH, Lee BH. Gene expression profiling in human lung fibroblast following cadmium exposure. Food Chem Toxicol 2008, 46(3):1131-1137.
25. Blain SW. Switching cyclin D-Cdk4 kinase activity on and off. Cell Cycle 2008, 7(7):892-898.
26. Lecomte C, Andujar P, Renier A, Kheuang L, Abramowski V, Mellottee L, Fleury-Feith J, Zucman-Rossi J, Giovannini M, Jaurand MC. Similar tumor suppressor gene alteration profiles in asbestos-induced murine and human mesothelioma. Cell Cycle 2005, 4(12):1862-1869.
27. Papp T, Schipper H, Pemsel H, Bastrop R, Muller KM, Wiethege T, Weiss DG, Dopp E, Schiffmann D, Rahman Q. Mutational analysis of N-ras, p53, p16INK4a, p14ARF and CDK4 genes in primary human malignant mesotheliomas. Int J Oncol 2001, 18(2):425-433.
28. Chen Y, Choong LY, Lin Q, Philp R, Wong CH, Ang BK, Tan YL, Loh MC, Hew CL, Shah N, et al. Differential expression of novel tyrosine kinase substrates during breast cancer development. Mol Cell Proteomics 2007, 6(12):2072-2087. 10.1074/mcp.M700395-MCP200, 17855441.
29. Sakhinia E, Glennie C, Hoyland JA, Menasce LP, Brady G, Miller C, Radford JA, Byers RJ. Clinical quantitation of diagnostic and predictive gene expression levels in follicular and diffuse large B-cell lymphoma by RT-PCR gene expression profiling. Blood 2007, 109(9):3922-3928. 10.1182/blood-2006-09-046391, 17255358.
30. Helleman J, Jansen MP, Span PN, van Staveren IL, Massuger LF, Meijer-van Gelder ME, Sweep FC, Ewing PC, Burg ME, Stoter G, et al. Molecular profiling of platinum resistant ovarian cancer. Int J Cancer 2006, 118(8):1963-1971. 10.1002/ijc.21599, 16287073.
31. Gasdaska PY, Gasdaska JR, Cochran S, Powis G. Cloning and sequencing of a human thioredoxin reductase. FEBS Lett 1995, 373(1):5-9. 10.1016/0014-5793(95)01003-W, 7589432.
32. Dammeyer P, Damdimopoulos AE, Nordman T, Jimenez A, Miranda-Vizuete A, Arner ES. Induction of cell membrane protrusions by the N-terminal glutaredoxin domain of a rare splice variant of human thioredoxin reductase 1. J Biol Chem 2008, 283(5):2814-2821. 10.1074/jbc.M708939200, 18042542.
33. Peters U, Chatterjee N, Hayes RB, Schoen RE, Wang Y, Chanock SJ, Foster CB. Variation in the selenoenzyme genes and risk of advanced distal colorectal adenoma. Cancer Epidemiol Biomarkers Prev 2008, 17(5):1144-1154. 10.1158/1055-9965.EPI-07-2947, 18483336.
34. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 2009, 19(9):1527-1541. 10.1101/gr.091868.109, 2752135, 19546169.