Targeting alternatively spliced sequence features for cancer diagnosis and therapeutics

Journal of Gastroenterology

Volumn 40, Issue , 2005, Pages 14-20

  Atanelov, Levan ^a   Xu, Qiang ^a   Rad, Ramin ^a   Lee, Christopher ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

alternative splicing; bioinformatics; cancer; diagnostics; genomics; tissue

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; BIOINFORMATICS; CANCER DIAGNOSIS; CANCER THERAPY; CARCINOGENESIS; CONTROLLED STUDY; DIAGNOSIS; GENOMICS; HUMAN; MAMMAL; NONHUMAN; EXPRESSED SEQUENCE TAG; GENE TARGETING; GENETICS; NEOPLASM; PROTEOMICS;

MESSENGER RNA;

ALTERNATIVE SPLICING; EXPRESSED SEQUENCE TAGS; GENE TARGETING; HUMANS; NEOPLASMS; PROTEOMICS; RNA, MESSENGER;

EID: 21844474567     PISSN: 09441174     EISSN: 14355922     Source Type: Journal    
DOI: 10.1007/BF02990573     Document Type: Article

References (36)

1. Maniatis T, Tanis B. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature (Lond) 2002; 418: 236–43. DOI: 10.1038/418236a
2. Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet 2002; 30: 13–9. DOI: 10.1038/ng0102-13
3. Mironov AA, Fickett JW, Gelfand MS. Frequent alternative splicing of human genes. Genome Res 1999; 9: 1288–93. DOI: 10.1101/gr.9.12.1288
4. Brett D, Hanke J, Lehmann G, Haase S, Delbruck S, Krueger S, et al. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett 2000; 474: 83–6. DOI: 10.1016/S0014-5793(00)01581-7
5. Croft L, Schandorff S, Clark F, Burrage K, Arctander P, Mattick JS. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat Genet 2000; 24: 340–1. DOI: 10.1038/74153
6. Consortium, IHGS. Initial sequencing and analysis of the human genome. Nature (Lond) 2001; 409: 860–921. DOI: 10.1038/35057062
7. Kan Z, Rouchka EC, Gish WR, States DJ. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 2001; 11: 889–900. DOI: 10.1101/gr.155001
8. Modrek B, Resch A, Grasso C, Lee C. Genome-wide analysis of alternative splicing using human expressed sequence data. Nucleic Acids Res 2001; 29: 2850–9. DOI: 10.1093/nar/29.13.2850
9. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, et al. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003; 302: 2141–4. DOI: 10.1126/science.1090100
10. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 2004;14: 331–42. DOI: 10.1101/gr.2094104
11. 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: 5635–43. DOI: 10.1093/nar/gkg786
12. Wang Z, Lo HS, Yang H, Gere S, Hu Y, Buetow KH, et al. Computational analysis and experimental validation of tumorassociated alternative RNA splicing in human cancer. Cancer Res 2003; 63: 655–7.
13. Ge K, DuHadaway J, Du W, Herlyn M, Rodeck U, Prendergast GC. Mechanism for elimination of a tumor suppressor: aberrant splicing of a brain-specific exon causes loss of function of Binl in melanoma. Proc Natl Acad Sci U S A 1999; 96: 9689–94. DOI: 10.1073/pnas.96.17.9689
14. Xia YF, Li YD, Li X, Geng JG. Identification of alternatively spliced Actl and implications for its roles in oncogenesis. Biochem Biophys Res Commun 2002; 296: 406–12. DOI: 10.1016/S0006-291X(02)00887-2
15. Whitman S, Wang X, Shalaby R, Shtivelman E. Alternatively spliced products CC3 and TC3 have opposing effects on apoptosis. Mol Cell Biol 2000; 20: 583–93. DOI: 10.1128/MCB.20.2.583-593.2000
16. Yamaguchi F, Saya H, Bruner JM, Morrison RS. Differential expression of two fibroblast growth factor-receptor genes is associated with malignant progression in human astrocytomas. Proc Natl Acad Sci U S A 1994; 91: 484–8. DOI: 10.1073/pnas.91.2.484
17. Koslowski M, Tureci O, Bell C, Krause P, Lehr HA, Brunner J, et al. Multiple splice variants of lactate dehydrogenase C selectively expressed in human cancer. Cancer Res 2002; 62: 6750–5.
18. Correa RG, de Carvalho AF, Pinheiro NA, Simpson AJ, de Souza SJ. NABC1 (BCAS1): alternative splicing and downregulation in colorectal tumors. Genomics 2000; 65: 299–302. DOI: 10.1006/geno.2000.6172
19. Saito H, Nakatsuru S, Inazawa J, Nishihira T, Park JG, Nakamura Y. Frequent association of alternative splicing of NER, a nuclear hormone receptor gene in cancer tissues. Oncogene 1997; 14: 617–21. DOI: 10.1038/sj.onc.1200859
20. Naor D, Nedvetzki S, Golan I, Melnik L, Faitelson Y. CD44 in cancer. Crit Rev Clin Lab Sci 2002; 39: 527–79. DOI: 10.1080/10408360290795574
21. Cragg MS, Chan HT, Fox MD, Tutt A, Smith A, Oscier DG, et al. The alternative transcript of CD79b is overexpressed in B-CLL and inhibits signaling for apoptosis. Blood 2002;100: 3068–76. DOI: 10.1182/blood.V100.9.3068
22. Castellani P, Borsi L, Carnemolla B, Biro A, Dorcaratto A, Viale GL, et al. Differentiation between high- and low-grade astrocytoma using a human recombinant antibody to the extra domain-B of fibronectin. Am J Pathol 2002;161: 1695–1700.
23. Feltes CM, Kudo A, Blaschuk O, Byers SW. An alternatively spliced cadherin-11 enhances human breast cancer cell invasion. Cancer Res 2002; 62: 6688–97.
24. Parareda A, Villaescusa JC, Sanchez de Toledo J, Gallego S. New splicing variants for human tyrosine hydroxylase gene with possible implications for the detection of minimal residual disease in patients with neuroblastoma. Neurosci Lett 2003; 336: 29–32. DOI: 10.1016/S0304-3940(02)01220-X
25. Chiarugi V, Del Rosso M, Magnelli L. Brn-3a, a neuronal transcription factor of the POU gene family: indications for its involvement in cancer and angiogenesis. Mol Biotechnol 2002; 22: 123–7. DOI: 10.1385/MB:22:2:123
26. Le Hir H, Charlet-Berguerand N, de Franciscis V, Thermes C. 5′-End RET splicing: absence of variants in normal tissues and intron retention in pheochromocytomas. Oncology 2002; 63: 84–91. DOI: 10.1159/000065725
27. Resch A, Xing Y, Modrek B, Gorlick M, Riley R, Lee C. Assess-ing the impact of alternative splicing on domain interactions in the human proteome. J Proteome Res 2004; 3: 76–83. DOI: 10.1021/pr034064v
28. Borjesson PK, Postema EJ, Roos JC, Colnot DR, Marres HA, van Schie MH, et al. Phase I therapy study with (186)Re-labeled humanized monoclonal antibody BIWA 4 (bivatuzumab) in patients with head and neck squamous cell carcinoma. Clin Cancer Res 2003; 9: 3961S-72S.
29. Tokue Y, Matsumura Y, Katsumata N, Watanabe T, Tarin D, Kakizoe T. CD44 variant isoform expression and breast cancer prognosis. Jpn J Cancer Res 1998; 89: 283–90.
30. Ghert MA, Jung ST, Qi W, Harrelson JM, Erickson HP, Block JA, et al. The clinical significance of tenascin-C splice variant expression in chondrosarcoma. Oncology 2001; 61: 306–14. DOI: 10.1159/000055338
31. van Der Velden VH, te Marvelde JG, Hoogeveen PG, Bernstein ID, Houtsmuller AB, Berger MS, et al. Targeting of the CD33-calicheamicin immunoconjugate Mylotarg (CMA-676) in acute myeloid leukemia: in vivo and in vitro saturation and internalization by leukemic and normal myeloid cells. Blood 2001; 97: 3197–204. DOI: 10.1182/blood.V97.10.3197
32. Carter P. Improving the efficacy of antibody-based cancer therapies. Nat Rev Cancer 2001; l: 118–29. DOI: 10.1038/35101072
33. Reff ME, Carner K, Chambers KS, Chinn PC, Leonard JE, Raab R, et al. Depletion of B cells in vivo by a chimeric mouse human monoclonal antibody to CD20. Blood 1994; 83: 435–45.
34. Blagosklonny MV. Tissue-selective therapy of cancer. Br J Cancer 2003; 89: 1147–51. DOI: 10.1038/sj.bjc.6601256
35. Xu Q, Modrek B, Lee C. Genome-wide detection of tissuespecific alternative splicing in the human transcriptome. Nucleic Acids Res 2002; 30: 3754–66. DOI: 10.1093/nar/gkf492
36. Biroccio A, Leonetti C, Zupi G. The future of antisense therapy: combination with anticancer treatments. Oncogene 2003; 22: 6579–88. DOI: 10.1038/sj.onc.1206812