Splice variants as cancer biomarkers

Clinical Biochemistry

Volumn 37, Issue 7, 2004, Pages 584-594

  Brinkman, Brigitta M N ^a,b  

^a ExonHit Therapeutics   (France)

^b NONE   (France)

Author keywords

Alternative splicing; Biomarker; Cancer; Diagnostics

Indexed keywords

TUMOR MARKER;

ALTERNATIVE RNA SPLICING; CANCER; CARCINOGENESIS; GENE MUTATION; GENETIC TRANSCRIPTION; HUMAN; MALIGNANT TRANSFORMATION; PRIORITY JOURNAL; REVIEW; TUMOR GROWTH;

ALTERNATIVE SPLICING; HUMANS; MODELS, BIOLOGICAL; MUTATION; NEOPLASMS; RNA, MESSENGER; RNA, NEOPLASM; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC; TUMOR MARKERS, BIOLOGICAL; VARIATION (GENETICS);

EID: 3042642783     PISSN: 00099120     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.clinbiochem.2004.05.015     Document Type: Review

References (72)

1. Wulfuhle J.D., Paweletz C.P., Steeg P.S., Petricoin E.F. III, Liotta L. Proteomic approaches to the diagnosis, treatment, and monitoring of cancer. Adv. Exp. Med. Biol. 532:2003;59-68
2. Macgregor P.F. Gene expression in cancer: the application of microarrays. Expert Rev. Mol. Diagn. 3:2003;185-200
3. Simon R., Radmacher M.D., Dobbin K., McShane L.M. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J. Natl. Cancer Inst. 95:2003;14-18
4. Diamandis E.P. Point: proteomic patterns in biological fluids: do they represent the future of cancer diagnostics? Clin. Chem. 49:2003;1272-1275
5. Black D.L. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72:2003;291-336
6. Maniatis T., Reed R. An extensive network of coupling among gene expression machines. Nature. 416:2002;499-506
7. Wu J.Y., Tang H., Havlioglu N. Alternative pre-mRNA splicing and regulation of programmed cell death. Prog. Mol. Subcell. Biol. 31:2003;153-185
8. Syken J., De-Medina T., Munger K. TID1, a human homolog of the Drosophila tumor suppressor l(2)tid, encodes two mitochondrial modulators of apoptosis with opposing functions. Proc. Natl. Acad. Sci. U. S. A. 96:1999;8499-8504
9. Jang J.H. Identification and characterization of soluble isoform of fibroblast growth factor receptor 3 in human SaOS-2 osteosarcoma cells. Biochem. Biophys. Res. Commun. 292:2002;378-382
10. Cartegni L., Chew S.L., Krainer A.R. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev., Genet. 3:2002;285-298
11. Ars E., Serra E., Garcia J., et al. Mutations affecting mRNA splicing are the most common molecular defects in patients with neurofibromatosis type 1. Hum. Mol. Genet. 9:2000;237-247
12. Ashkenas J. Gene regulation by mRNA editing. Am. J. Hum. Genet. 60:1997;278-283
13. Maas S., Patt S., Schrey M., Rich A. Underediting of glutamate receptor GluR-B mRNA in malignant gliomas. Proc. Natl. Acad. Sci. U. S. A. 98:2001;14687-14692
14. Beghini A., Ripamonti C.B., Peterlongo P., et al. RNA hyperediting and alternative splicing of hematopoietic cell phosphatase (PTPN6) gene in acute myeloid leukemia. Hum. Mol. Genet. 9:2000;2297-2304
15. Daoud R., Stoilov P., Stoss O., et al. Controls of pre-mRNA processing by extracellular signals: emerging molecular mechanisms. Gene Ther. Mol. Biol. 5:2000;121-130
16. Stickeler E., Kittrell F., Medina D., Berget S.M. Stage-specific changes in SR splicing factors and alternative splicing in mammary tumorigenesis. Oncogene. 18:1999;3574-3582
17. Chalfant C.E., Rathman K., Pinkerman R.L., et al. De novo ceramide regulates the alternative splicing of caspase 9 and Bcl-x in A549 lung adenocarcinoma cells. Dependence on protein phosphatase-1. J. Biol. Chem. 277:2002;12587-12595
18. Jin W., Bruno I.G., Xie T.X., Sanger L.J., Cote G.J. Polypyrimidine tract-binding protein down-regulates fibroblast growth factor receptor 1 alpha-exon inclusion. Cancer Res. 63:2003;6154-6157
19. Jin W., McCutcheon I.E., Fuller G.N., Huang E.S., Cote G.J. Fibroblast growth factor receptor-1 alpha-exon exclusion and polypyrimidine tract-binding protein in glioblastoma multiforme tumors. Cancer Res. 60:2000;1221-1224
20. Wollerton M.C., Gooding C., Robinson F., Brown E.C., Jackson R.J., Smith C.W. Differential alternative splicing activity of isoforms of polypyrimidine tract binding protein (PTB). RNA. 7:2001;819-832
21. Jiang Z.H., Zhang W.J., Rao Y., Wu J.Y. Regulation of Ich-1 pre-mRNA alternative splicing and apoptosis by mammalian splicing factors. Proc. Natl. Acad. Sci. U. S. A. 95:1998;9155-9160
22. Logette E., Wotawa A., Solier S., Desoche L., Solary E., Corcos L. The human caspase-2 gene: alternative promoters, pre-mRNA splicing and AUG usage direct isoform-specific expression. Oncogene. 22:2003;935-946
23. Cramer P., Pesce C.G., Baralle F.E., Kornblihtt A.R. Functional association between promoter structure and transcript alternative splicing. Proc. Natl. Acad. Sci. U. S. A. 94:1997;11456-11460
24. 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. 55:2003;235-241
25. Kadener S., Cramer P., Nogues G., et al. Antagonistic effects of T-Ag and VP16 reveal a role for RNA pol II elongation on alternative splicing. EMBO J. 20:2001;5759-5768
26. Zauberman A., Flusberg D., Haupt Y., Barak Y., Oren M. A functional p53-responsive intronic promoter is contained within the human mdm2 gene. Nucleic Acids Res. 23:1995;2584-2592
27. Naor D., Nedvetzki S., Golan I., Melnik L., Faitelson Y. CD44 in cancer. Crit. Rev. Clin. Lab. Sci. 39:2002;527-579
28. Yakushijin Y., Steckel J., Kharbanda S., et al. A directly spliced exon 10-containing CD44 variant promotes the metastasis and homotypic aggregation of aggressive non-Hodgkin's lymphoma. Blood. 91:1998;4282-4291
29. Iida N., Bourguignon L.Y. Coexpression of CD44 variant (v10/ex14) and CD44S in human mammary epithelial cells promotes tumorigenesis. J. Cell. Physiol. 171:1997;152-160
30. Jiang H., Knudson C.B., Knudson W. Antisense inhibition of CD44 tailless splice variant in human articular chondrocytes promotes hyaluronan internalization. Arthritis Rheum. 44:2001;2599-2610
31. Kuniyasu H., Oue N., Tsutsumi M., Tahara E., Yasui W. Heparan sulfate enhances invasion by human colon carcinoma cell lines through expression of CD44 variant exon 3. Clin. Cancer Res. 7:2001;4067-4072
32. Stroomer J.W., Roos J.C., Sproll M., et al. Safety and biodistribution of 99mTechnetium-labeled anti-CD44v6 monoclonal antibody BIWA 1 in head and neck cancer patients. Clin. Cancer Res. 6:2000;3046-3055
33. Navaglia F., Fogar P., Greco E., et al. CD44v10: an antimetastatic membrane glycoprotein for pancreatic cancer. Int. J. Biol. Markers. 18:2003;130-138
34. Xin Y., Grace A., Gallagher M.M., Curran B.T., Leader M.B., Kay E.W. CD44V6 in gastric carcinoma: a marker of tumor progression. Appl. Immunohistochem. Mol. Morphol. 9:2001;138-142
35. Aaltomaa S., Lipponen P., Ala-Opas M., Kosma V.M. Expression and prognostic value of CD44 standard and variant v3 and v6 isoforms in prostate cancer. Eur. Urol. 39:2001;138-144
36. Iczkowski K.A., Bai S., Pantazis C.G. Prostate cancer overexpresses CD44 variants 7-9 at the messenger RNA and protein level. Anticancer Res. 23:2003;3129-3140
37. Lee S.C., Harn H.J., Lin T.S., et al. Prognostic significance of CD44v5 expression in human thymic epithelial neoplasms. Ann. Thorac. Surg. 76:2003;213-218
38. Kim H.S., Park Y.B., Oh J.H., Jeong J., Kim C.J., Lee S.H. Expression of CD44 isoforms correlates with the metastatic potential of osteosarcoma. Clin. Orthop. 396:2002;184-190
39. Shimbori M., Kijima H., Sato S., et al. Expression of CD44 in primary lung carcinomas using histological and cytological analyses. Anticancer Res. 23:2003;115-121
40. Wagner K.D., Wagner N., Schedl A. The complex life of WT1. J. Cell Sci. 116:2003;1653-1658
41. Baudry D., Hamelin M., Cabanis M.O., et al. WT1 splicing alterations in Wilms' tumors. Clin. Cancer Res. 6:2000;3957-3965
42. Hammes A., Guo J.K., Lutsch G., et al. Two splice variants of the Wilms' tumor 1 gene have distinct functions during sex determination and nephron formation. Cell. 106:2001;319-329
43. Powell S.N., Kachnic L.A. Roles of BRCA1 and BRCA2 in homologous recombination, DNA replication fidelity and the cellular response to ionizing radiation. Oncogene. 22:2003;5784-5791
44. Claes K., Poppe B., Machackova E., et al. Differentiating pathogenic mutations from polymorphic alterations in the splice sites of BRCA1 and BRCA2. Genes Chromosomes Cancer. 37:2003;314-320
45. Lu M., Conzen S.D., Cole C.N., Arrick B.A. Characterization of functional messenger RNA splice variants of BRCA1 expressed in nonmalignant and tumor-derived breast cells. Cancer Res. 56:1996;4578-4581
46. Thakur S., Zhang H.B., Peng Y., et al. Localization of BRCA1 and a splice variant identifies the nuclear localization signal. Mol. Cell. Biol. 17:1997;444-452
47. Bieche I., Lidereau R. Increased level of exon 12 alternatively spliced BRCA2 transcripts in tumor breast tissue compared with normal tissue. Cancer Res. 59:1999;2546-2550
48. Deb S.P. Function and dysfunction of the human oncoprotein MDM2. Front. Biosci. 7:2002;d235-d243
49. Evans S.C., Viswanathan M., Grier J.D., Narayana M., El-Naggar A.K., Lozano G. An alternatively spliced HDM2 product increases p53 activity by inhibiting HDM2. Oncogene. 20:2001;4041-4049
50. Bartel F., Taubert H., Harris L.C. Alternative and aberrant splicing of MDM2 mRNA in human cancer. Cancer Cell. 2:2002;9-15
51. Hori M., Shimazaki J., Inagawa S., Itabashi M., Hori M. Alternatively spliced MDM2 transcripts in human breast cancer in relation to tumor necrosis and lymph node involvement. Pathol. Int. 50:2000;786-792
52. Heuze-Vourc'h N., Leblond V., Courty Y. Complex alternative splicing of the hKLK3 gene coding for the tumor marker PSA (prostate-specific-antigen). Eur. J. Biochem. 270:2003;706-714
53. Yousef G.M., Diamandis E.P. The new human tissue kallikrein gene family: structure, function, and association to disease. Endocr. Rev. 22:2001;184-204
54. Kwiatkowski M.K., Recker F., Piironen T., et al. In prostatism patients the ratio of human glandular kallikrein to free PSA improves the discrimination between prostate cancer and benign hyperplasia within the diagnostic "gray zone" of total PSA 4 to 10 ng/mL. Urology. 52:1998;360-365
55. Heese A., Becker C., Noldus J., et al. Human glandular kallikreins 2: a potential serum marker for predicting the organ confined vs. non-organ confined growth of prostate cancer. J. Urol. 163:2000;1491-1497
56. Slawin K.M., Shariat S.F., Nguyen C., et al. Detection of metastatic prostate cancer using a splice variant-specific reverse transcriptase-polymerase chain reaction assay for human glandular kallikrein. Cancer Res. 60:2000;7142-7148
57. Chang A., Yousef G.M., Jung K., Rajpert-De Meyts E., Diamandis E.P. Identification and molecular characterization of five novel kallikrein gene 13 (KLK13; KLK-L4) splice variants: differential expression in the human testis and testicular cancer. Anticancer Res. 21:2001;3147-3352
58. Dong Y., Kaushal A., Brattsand M., Nicklin J., Clements J.A. Differential splicing of KLK5 and KLK7 in epithelial ovarian cancer produces novel variants with potential as cancer biomarkers. Clin. Cancer Res. 9:2003;1710-1720
59. Nakamura T., Stephan C., Scorilas A., Yousef G.M., Jung K., Diamandis E.P. Quantitative analysis of hippostasin/KLK11 gene expression in cancerous and noncancerous prostatic tissues. Urology. 61:2003;1042-1046
60. Yeh B.K., Igarashi M., Eliseenkova A.V., Plotnikov A.N., Sher I., Ron D., et al. Structural basis by which alternative splicing confers specificity in fibroblast growth factor receptors. Proc. Natl. Acad. Sci. U. S. A. 100:2003;2266-2271
61. Ezzat S., Zheng L., Yu S., Asa S.L. A soluble dominant negative fibroblast growth factor receptor 4 isoform in human MCF-7 breast cancer cells. Biochem. Biophys. Res. Commun. 287:2001;60-65
62. Vickers S.M., Huang Z.Q., MacMillan-Crow L., Greendorfer J.S., Thompson J.A. Ligand activation of alternatively spliced fibroblast growth factor receptor-1 modulates pancreatic adenocarcinoma cell malignancy. J. Gastrointest. Surg. 6:2002;546-553
63. Jang J.H., Shin K.H., Park J.G. Mutations in fibroblast growth factor receptor 2 and fibroblast growth factor receptor 3 genes associated with human gastric and colorectal cancers. Cancer Res. 61:2001;3541-3543
64. Kwabi-Addo B., Ropiquet F., Giri D., Ittmann M. Alternative splicing of fibroblast growth factor receptors in human prostate cancer. Prostate. 46:2001;163-172
65. Abbass S.A., Asa S.L., Ezzat S. Altered expression of fibroblast growth factor receptors in human pituitary adenomas. J. Clin. Endocrinol. Metab. 82:1997;1160-1166
66. Modrek B., Resch A., Grasso C., Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29:2001;2850-2859
67. Xie H., Zhu W.Y., Wasserman A., Grebinskiy V., Olson A., Mintz L. Computational analysis of alternative splicing using EST tissue information. Genomics. 80:2002;326-330
68. Xu Q., Lee C. Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res. 31:2003;5635-5643
69. Schweighoffer F., Ait-Ikhlef A., Resink A., et al. Qualitative gene profiling: a novel tool in genomics and in pharmacogenomics that deciphers messenger RNA isoforms diversity. Pharmacogenomics. 1:2000;187-197
70. Hisatomi H., Nagao K., Kawakita M., et al. Detection of circulating prostate tumor cells: alternative spliced variant of PSM induced false-positive result. Int. J. Mol. Med. 10:2002;619-622
71. Yeakley J.M., Fan J.B., Doucet D., Luo L., Wickham E., Ye Z., et al. Profiling alternative splicing on fiber-optic arrays. Nat. Biotechnol. 20:2002;353-358
72. Clark T.A., Sugnet C.W., Ares M. Jr. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science. 296:2002;907-910