Alternative isoform discrimination by the next generation of expression profiling microarrays

Expert Opinion on Therapeutic Targets

Volumn 10, Issue 4, 2006, Pages 613-625

  Pando, Matthew P ^a   Kotraiah, Vinayaka ^a   McGowan, Kevin ^b   Bracco, Laurent ^c   Einstein, Richard ^a  

^a ExonHit Therapeutics Inc   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c ExonHit Therapeutics   (France)

Author keywords

Alternative splicing; DNA microarray; Exon; Expression profiling; Intron; Junction; Transcriptome

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; CHLORIDE CHANNEL; COMPLEMENTARY DNA; INSULIN RECEPTOR; MESSENGER RNA; NEUROFIBROMIN; OLIGONUCLEOTIDE; PROTEIN BCL XL; SURVIVAL MOTOR NEURON PROTEIN; TROPONIN T;

5' UNTRANSLATED REGION; ACCURACY; AMPLICON; ARTICLE; AUTOSOMAL DOMINANT DISORDER; CARCINOGENESIS; DNA MICROARRAY; DRUG TARGETING; EXON; GENE EXPRESSION PROFILING; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; GENE TECHNOLOGY; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME; HUMAN; MYOTONIC DYSTROPHY; NONHUMAN; POLYMERASE CHAIN REACTION; PROTEIN FUNCTION; RETINITIS PIGMENTOSA;

ALTERNATIVE SPLICING; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN ISOFORMS;

EID: 33746728203     PISSN: 14728222     EISSN: None     Source Type: Journal    
DOI: 10.1517/14728222.10.4.613     Document Type: Article

References (105)

1. VENTER JC, ADAMS MD, MYERS EW et al.: The sequence of the human genome. Science (2001) 291(5507):1304-1351.
2. LANDER ES: Initial sequencing and analysis of the human genome. Nature (2001) 409:860-921.
3. HARRISON PM, KUMAR A, LANG N, SNYDER M, GERSTEIN M: A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res. (2002) 30(5):1083-1090.
4. 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.
5. MODREK B, LEE C: A genomic view of alternative splicing. Nat. Genet. (2002) 30(1):13-19.
6. KAMPA D, CHENG J, KAPRANOV P et al.: Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. (2004) 14(3):331-342.
7. GRABOWSKI PJ, BLACK DL: Alternative RNA splicing in the nervous system. Prog. Neurobiol. (2001) 65(3):289-308.
8. FAUSTINO NA, COOPER TA: Pre-mRNA splicing and human disease. Genes Dev. (2003) 17(4):419-437.
9. GARCIA-BLANCO MA, BARANIAK AP, LASDA EL: Alternative splicing in disease and therapy. Nat. Biotechnol. (2004) 22(5):535-546.
10. STENSON PD, BALL EV, MORT M et al.: Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat. (2003) 21(6):577-581.
11. LOPEZ-BIGAS N, AUDIT B, OUZOUNIS C, PARRA G, GUIGO R: Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett. (2005) 579(9):1900-1903.
12. CHAUDHURI JD: Genes arrayed out for you: the amazing world of microarrays. Med. Sci. Monit. (2005) 11(2):RA52-RA62.
13. PENNIE WD: Custom cDNA microarrays; technologies and applications. Toxicology (2002) 181-182:551-554.
14. STOUGHTON RB: Applications of DNA microarrays in biology. Ann. Rev. Biochem. (2005) 74:53-82.
15. MOCKLER TC, CHAN S, SUNDARESAN A, CHEN H, JACOBSEN SE, ECKER JR: Applications of DNA tiling arrays for whole-genome analysis. Genomics (2005) 85(1):1-15.
16. MANTRIPRAGADA KK, BUCKLEY PG, DE STAHL TD, DUMANSKI JP: Genomic microarrays in the spotlight. Trends Genet. (2004) 20(2):87-94.
17. HEDENFALK I, RINGNER M, BEN-DOR A et al.: Molecular classification of familial non-BRCA1/BRCA2 breast cancer. Proc. Natl. Acad. Sci. USA (2003) 100(5):2532-2537.
18. BRUNET JP, TAMAYO P, GOLUB TR, MESIROV JP: Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. USA (2004) 101(12):4164-4169.
19. POMEROY SL, TAMAYO P, GAASENBEEK M et al.: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 415(6870):436-442.
20. CLARKE PA, TE POELE R, WORKMAN P: Gene expression microarray technologies in the development of new therapeutic agents. Eur. J. Cancer. (2004) 40(17):2560-2591.
21. ROBERT J, VEKRIS A, POURQUIER P, BONNET J: Predicting drug response based on gene expression. Crit. Rev. Oncol. Hematol. (2004) 51(3):205-227.
22. HAMADEH HK, AMIN RP, PAULES RS, AFSHARI CA: An overview of toxicogenomics. Curr. Issues Mol. Biol. (2002) 4(2):45-56.
23. LIGUORI MJ, ANDERSON LM, BUKOFZER S et al.: Microarray analysis in human hepatocytes suggests a mechanism for hepatotoxicity induced by trovafloxacin. Hepatology (2005) 41(1):177-186.
24. BLUME J: Capturing the diversity of transcript variation using exon arrays. In: CHI Molecular Medicine Tri-conference (2005).
25. CLINE MS, BLUME J, CAWLEY S et al.: ANOSVA: a statistical method for detecting splice variation from expression data. Bioinformatics (2005) 21(Suppl. 1):i107-i115.
26. BLANCHETTE M, GREEN RE, BRENNER SE, RIO DC: Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev. (2005) 19(11):1306-1314.
27. LE K, MITSOURAS K, ROY M et al.: Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res. (2004) 32(22):e180.
28. PAN Q, SHAI O, MISQUITTA C et al.: Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell. (2004) 16(6):929-941.
29. JOHNSON JM, CASTLE J, GARRETT-ENGELE P et al.: Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (2003) 302(5653):2141-2144.
30. SHOEMAKER DD, SCHADT EE, ARMOUR CD et al.: Experimental annotation of the human genome using microarray technology. Nature (2001) 409(6822):922-927.
31. HU GK, MADORE SJ, MOLDOVER B et al.: Predicting splice variant from DNA chip expression data. Genome Res. (2001) 11(7):1237-45.
32. WANG H, HUBBELL E, HU JS et al.: Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics (2003) 19(Suppl. 1):i315-i322.
33. CASTLE J, GARRETT-ENGELE P, ARMOUR CD et al.: Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol. (2003) 4(10):R66.
34. KAN Z, STATES D, GISH W: Selecting for functional alternative splices in ESTs. Genome Res. (2002) 12(12):1837-1845.
35. WANG Z, LO HS, YANG H et al.: Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer. Cancer Res. (2003) 63(3):655-657.
36. XU Q, MODREK B, LEE C: Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res. (2002) 30(17):3754-3766.
37. XU Q, LEE C: Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res. (2003) 31(19):5635-5643.
38. HINRICHS AS, KAROLCHIK D, BAERTSCH R et al.: The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. (2006) 34(Database issue):D590-D598.
39. KAROLCHIK D, BAERTSCH R, DIEKHANS M et al.: The UCSC genome browser database. Nucleic Acids Res. (2003) 31(1):51-54.
40. KENT WJ, SUGNET CW, FUREY TS et al.: The human genome browser at UCSC. Genome Res. (2002) 12(6):996-1006.
41. KENT WJ: BLAT-the BLAST-like alignment tool. Genome Res. (2002) 12(4):656-664.
42. FEHLBAUM P, GUIHAL C, BRACCO L, COCHET O: A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res. (2005) 33(5):e47.
43. ZHANG W, MORRIS QD, CHANG R et al.: The functional landscape of mouse gene expression. J. Biol. (2004) 3(5):21.
44. CLARK TA, SUGNET CW, ARES M Jr: Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science (2002) 296(5569):907-910.
45. KRAWCZAK M, REISS J, COOPER DN: The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences. Hum. Genet. (1992) 90(1-2):41-54.
46. DARREH-SHORI T, HELLSTROM-LINDAHL E, FLORES-FLORES C, GUAN ZZ, SOREQ H, NORDBERG A: Long-lasting acetylcholinesteraae splice variations in anticholinesterase-treated Alzheimer's disease patients. J. Neurochem. (2004) 88(5):1102-1113.
47. STETEFELD J, RUEGG MA: Structural and functional diversity generated by alternative mRNA splicing. Trends Biochem. Sci. (2005) 30(9):515-521.
48. SMITH CW, VALCARCEL J: Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci. (2000) 25(8):381-388.
49. TAZI J, DURAND S, JEANTEUR P: The spliceosome: a novel multi-faceted target for therapy. Trends Biochem. Sci. (2005) 30(8):469-478.
50. STAMM S, BEN-ARI S, RAFALSKA I et al.: Function of alternative splicing. Gene (2005) 344:1-20.
51. MIRIAMI E, SPERLING R, SPERLING J, MOTRO U: Regulation of splicing: the importance of being translatable. RNA (2004) 10(1):1-4.
52. NOGUES G, KADENER S, CRAMER P et al.: Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. IUBMB Life (2003) 55(4-5):235-241.
53. ROBERTS GC, SMITH CW: Alternative splicing: combinatorial output from the genome. Curr. Opin. Chem. Biol. (2002) 6(3):375-383.
54. CACERES JF, KORNBLIHTT AR: Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet. (2002) 18(4):186-193.
55. TAYLOR JK, ZHANG QQ, WYATT JR, DEAN NM: Induction of endogenous Bcl-xS through the control of Bcl-x pre-mRNA splicing by antisense oligonucleotides. Nat. Biotechnol. (1999) 17(11):1097-1100.
56. ROHRBACH S, MULLER-WERDAN U, WERDAN K, KOCH S, GELLERICH NF, HOLTZ J: Apoptosis-modulating interaction of the neuregulin/erbB pathway with antracyclines in regulating Bcl-xS and Bcl-xL in cardiomyocytes. J. Mol. Cell. Cardiol. (2005) 38(3):485-493.
57. SATAGOPAN JM, OFFIT K, FOULKES W et al.: The lifetime risks of breast cancer in Ashkenazi Jewish carriers of BRCA1 and BRCA2 mutations. Cancer Epidemiol. Biomarkers Prev. (2001) 10(5):467-473.
58. FORD D, EASTON DF, BISHOP DT, NAROD SA, GOLDGAR DE: Risks of cancer in BRCA1-mutation carriers. Breast Cancer Linkage Consortium. Lancet (1994) 343(8899):692-695.
59. FORD D, EASTON DF, STRATTON M et al.: Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am. J. Hum. Genet. (1998) 62(3):676-689.
60. STRUEWING JP, HARTGE P, WACHOLDER S et al.: The risk of cancer associated with specific mutations of BRCA1 and BRCA2 among Ashkenazi Jews. N. Engl. J. Med. (1997) 336(20):1401-1408.
61. THORLACIUS S, STRUEWING JP, HARTGE P et al.: Population-based study of risk of breast cancer in carriers of BRCA2 mutation. Lancet (1998) 352(9137):1337-1339.
62. ANTONIOU AC, GAYTHER SA, STRATTON JF, PONDER BA, EASTON DF: Risk models for familial ovarian and breast cancer. Genet. Epidemiol. (2000) 18(2):173-190.
63. MAZOYER S, PUGET N, PERRIN-VIDOZ L, LYNCH HT, SEROVA-SINILNIKOVA OM, LENOIR GM: A BRCA1 nonsense mutation causes exon skipping. Am. J. Hum. Genet. (1998) 62(3):713-715.
64. LIU HX, CARTEGNI L, ZHANG MQ, KRAINER AR: A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nat. Genet. (2001) 27(1):55-58.
65. FACKENTHAL JD, CARTEGNI L, KRAINER AR, OLOPADE OI: BRCA2 T2722R is a deleterious allele that causes exon skipping. Am. J. Hum. Genet. (2002) 71(3):625-631.
66. KING MC, MARKS JH, MANDELL JB: Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science (2003) 302(5645):643-646.
67. CONNELL JW, RODRIGUEZ-MARTIN T, GIBB GM et al.: Quantitative analysis of tau isoform transcripts in sporadic tauopathies. Brain Res. Mol. Brain Res. (2005) 137(1-2):104-109.
68. MILES C, ELGAR G, COLES E, KLEINJAN DJ, VAN HEYNINGEN V, Hastie N: Complete sequencing of the Fugu WAGR region from WT1 to PAX6: dramatic compaction and conservation of synteny with human chromosome 11p13. Proc. Natl. Acad. Sci. USA (1998) 95(22):13068-13072.
69. HABER DA, SOHN RL, BUCKLER AJ, PELLETIER J, CALL KM, HOUSMAN DE: Alternative splicing and genomic structure of the Wilms tumor gene WT1. Proc. Natl. Acad. Sci. USA (1991) 88(21):9618-9622.
70. HOSSAIN A, SAUNDERS GF: The human sex-determining gene SRY is a direct target of WT1. J. Biol. Chem. (2001) 276(20):16817-16823.
71. WILHELM D, ENGLERT C: The Wilms tumor suppressor WT1 regulates early gonad development by activation of Sf1. Genes Dev. (2002) 16(14):1839-1851.
72. BARBAUX S, NIAUDET P, GUBLER MC et al.: Donor splice-site mutations in WT1 are responsible for Frasier syndrome. Nat. Genet. (1997) 17(4):467-470.
73. SUWANMANEE T, SIERAKOWSKA H, FUCHAROEN S, KOLE R: Repair of a splicing defect in erythroid cells from patients with beta-thalassemia/HbE disorder. Mol. Ther. (2002) 6(6):718-726.
74. VALENTINE CR: The association of nonsense codons with exon skipping. Mutat. Res. (1998) 411(2):87-117.
75. CARTEGNI L, CHEW SL, KRAINER AR: Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet. (2002) 3(4):285-298.
76. ORBAN TI, OLAH E: Emerging roles of BRCA1 alternative splicing. Mol. Pathol. (2003) 56(4):191-197.
77. LI F: Role of survivin and its splice variants in tumorigenesis. Br. J. Cancer. (2005) 92(2):212-216.
78. KALNINA Z, ZAYAKIN P, SILINA K, LINE A: Alterations of pre-mRNA splicing in cancer. Genes Chromosomes Cancer (2005) 42(4):342-357.
79. KNUDSEN KE, DIEHL JA, HAIMAN CA, KNUDSEN ES: Cyclin D1: polymorphism, aberrant splicing and cancer risk. Oncogene (2006) 25(11):1620-1628.
80. ZHOU Z, LICKLIDER LJ, GYGI SP, REED R: Comprehensive proteomic analysis of the human spliceosome. Nature (2002) 419(6903):182-185.
81. MANKODI A, THORNTON CA: Myotonic syndromes. Curr. Opin. Neurol. (2002) 15(5):545-552.
82. HARPER PS: Myotonic dystrophy, W.B. Sanders, London UK (2001).
83. MANKODI A, LOGIGIAN E, CALLAHAN L et al.: Myotonic dystrophy in transgenic mice expressing an expanded CUG repeat. Science (2000) 289(5485):1769-1773.
84. SAVKUR RS, PHILIPS AV, COOPER TA: Aberrant regulation of insulin receptor alternative splicing is associated with insulin resistance in myotonic dystrophy. Nat. Genet. (2001) 29(1):40-47.
85. CHARLET BN, SAVKUR RS, SINGH G, PHILIPS AV, GRICE EA, COOPER TA: Loss of the muscle-specific chloride channel in Type 1 myotonic dystrophy due to misregulated alternative splicing. Mol. Cell. (2002) 10(1):45-53.
86. LORSON CL, HAHNEN E, ANDROPHY EJ, WIRTH B: A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. Proc. Natl. Acad. Sci. USA (1999) 96(11):6307-6311.
87. WOLSTENCROFT EC, MATTIS V, BAJER AA, YOUNG PJ, LORSON CL: A non-sequence-specific requirement for SMN protein activity: the role of aminoglycosides in inducing elevated SMN protein levels. Hum. Mol. Genet. (2005) 14(9):1199-1210.
88. ROSSOLL W, KRONING AK, OHNDORF UM, STEEGBORN C, JABLONKA S, SENDTNER M: Specific interaction of Smn, the spinal muscular atrophy determining gene product, with hnRNP-R and gry-rbp/hnRNP-Q: a role for Smn in RNA processing in motor axons? Hum. Mol. Genet. (2002) 11(1):93-105.
89. SUMNER CJ, HUYNH TN, MARKOWITZ JA et al.: Valproic acid increases SMN levels in spinal muscular atrophy patient cells. Ann. Neurol. (2003) 54(5):647-654.
90. BRICHTA L, HOFMANN Y, HAHNEN E et al.: Valproic acid increases the SMN2 protein level: a well-known drug as a potential therapy for spinal muscular atrophy. Hum. Mol. Genet. (2003) 12(19):2481-2489.
91. MADOCSAI C, LIM SR, GEIB T, LAM BJ, HERTEL KJ: Correction of SMN2 Pre-mRNA splicing by antisense U7 small nuclear RNAs. Mol. Ther. (2005) 12(6):1013-1022.
92. JARECKI J, CHEN X, BERNARDINO A et al.: Diverse small-molecule modulators of SMN expression found by high-throughput compound screening: early leads towards a therapeutic for spinal muscular atrophy. Hum. Mol. Genet. (2005) 14(14):2003-2018.
93. STREULI M, HALL LR, SAGA Y, SCHLOSSMAN SF, SAITO H: Differential usage of three exons generates at least five different mRNAs encoding human leukocyte common antigens. J. Exp. Med. (1987) 166(5):1548-1566.
94. GRAVES PN, GRABOWSKI GA, LUDMAN MD, PALESE P, SMITH FI: Human acid beta-glucosidase: northern blot and S1 nuclease analysis of mRNA from HeLa cells and normal and Gaucher disease fibroblasts. Am. J. Hum. Genet. (1986) 39(6):763-774.
95. MAGKLARA A, SCORILAS A, KATSAROS D et al.: The human KLK8 (neuropsin/ ovasin) gene: identification of two novel splice variants and its prognostic value in ovarian cancer. Clin. Cancer Res. (2001) 7(4):806-811.
96. PEREZ C, VANDESOMPELE J, VANDENBROUCKE I et al.: Quantitative real time polymerase chain reaction for measurement of human interleukin-5 receptor alpha spliced isoforms mRNA. BMC Biotechnol. (2003) 3(1):17.
97. TOO HP: Real time PCR quantification of GFRalpha-2 alternatively spliced isoforms in murine brain and peripheral tissues. Brain Res. Mol. Brain Res. (2003) 114(2):146-153.
98. MARCHUK DA, SAULINO AM, TAVAKKOL R et al.: eDNA cloning of the Type 1 neurofibromatosis gene: complete sequence of the NF1 gene product. Genomics (1991) 11(4):931-940.
99. VANDENBROUCKE, II, VANDESOMPELE J, PAEPE AD, MESSIAEN L: Quantification of splice variants using real-time PCR. Nucleic Acids Res. (2001) 29(13):E68-E68.
100. WIEDMANN M, WILSON WJ, CZAJKA J, LUO J, BARANY F, BATT CA: Ligase chain reaction (LCR)-overview and applications. PCR Methods Appl. (1994) 3(4):S51-S64.
101. SAMOWITZ WS, THLIVERIS A, SPIRIO LN, WHITE R: Alternatively spliced adenomatous polyposis coli (APC) gene transcripts that delete exons mutated in attenuated APC. Cancer Res. (1995) 55(17):3732-3734.
102. SCHWEIGHOFFER F, AIT-IKHLEF A, RESINK AL et al.: Qualitative gene profiling: a novel tool in genomics and in pharmacogenomics that deciphers messenger RNA isoforms diversity. Pharmacogenomics (2000) 1(2):187-197.
103. CELOTTO AM, LEE JW, GRAVELEY BR: Exon-specific RNA interference: a tool to determine the functional relevance of proteins encoded by alternatively spliced mRNAs. Methods Mol. Biol. (2005) 309:273-282.
104. KISIELOW M, KLEINER S, NAGASAWA M, FAISAL A, NAGAMINE Y: Isoform-specific knockdown and expression of adaptor protein ShcA using small interfering RNA. Biochem. J. (2002) 363(Pt 1):1-5.
105. LINDSAY MA: Finding new drug targets in the 21st century. Drug Discov. Today (2005) 10(23-24):1683-1687.