Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis

PLoS Computational Biology

Volumn 5, Issue 11, 2009, Pages

  Moller Levet, Carla S ^a,b   Betts, Guy N J ^b   Harris, Adrian L ^c   Homer, Jarrod J ^d   West, Catharine M L ^b   Miller, Crispin J ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c JOHN RADCLIFFE HOSPITAL   (United Kingdom)

^d UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DIAGNOSIS; DISEASES; GENE EXPRESSION;

ALTERNATIVE SPLICING; ARRAY ANALYSIS; BIOLOGICAL PROCESS; CANCER BIOLOGY; HEAD-AND-NECK CANCER; HEAD-AND-NECK SQUAMOUS CELL CARCINOMA; LAMININ; SAMPLE DATASET; SPLICE VARIANTS; TUMOR CELL INVASION;

TUMORS;

BIOLOGICAL MARKER; LAMININ; LAMININ ALPHA3; UNCLASSIFIED DRUG; LAMININ ALPHA 3;

ALTERNATIVE RNA SPLICING; ARTICLE; CANCER GROWTH; CANCER INVASION; CONTROLLED STUDY; DISEASE ASSOCIATION; DISEASE MARKER; EXON; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE LOCUS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HEAD AND NECK CANCER; HUMAN; HUMAN CELL; HYPOXIA; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; PROGNOSIS; PROSPECTIVE STUDY; QUALITATIVE ANALYSIS; RELIABILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SQUAMOUS CELL CARCINOMA; VALIDATION PROCESS; ANOXIA; CLUSTER ANALYSIS; DNA MICROARRAY; DNA SEQUENCE; GENETICS; HEAD AND NECK TUMOR; METABOLISM; RNA SPLICING; TUMOR CELL LINE;

ALTERNATIVE SPLICING; ANOXIA; CARCINOMA, SQUAMOUS CELL; CELL LINE, TUMOR; CLUSTER ANALYSIS; EXONS; GENE EXPRESSION REGULATION, NEOPLASTIC; HEAD AND NECK NEOPLASMS; HUMANS; LAMININ; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA SPLICING; SEQUENCE ANALYSIS, DNA;

EID: 73449118582     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000571     Document Type: Article

References (44)

1. Clark F, Thanaraj TA (2002) Categorization and characterization of transcriptconfirmed consitutively and alternatively spliced introns and exons from human. Human Molecular Genetics 11: 451-464.
2. Gardina PJ (2006) Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 7: 325.
3. Johnson J, Castle J, Garrett-Engele P, Kan Z, Loerch P, et al. (2003) Genomewide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302: 2141-2144.
4. Hanahan D, Weinberg R (2000) The hallmarks of cancer. Cell 100: 57-70.
5. Venables-2006 (2006) Unbalanced alternative splicing and its significance in cancer. Bioessays 28: 378-386.
6. Zhang X, Liu G, Lengurg ME, Spira A (2007) Comparison of smoking-induced gene expression on Affymetrix Exon and 39-based expression arrays. Genome Informatics 18: 247-257.
7. Okoniewski MJ, Yates T, Dibben S, Miller CJ (2007) An annotation infractructure for the analysis and interpretation of Affymetrix exon array data. Genome Biology 8: R79.
8. Okoniewski MJ, Miller CJ (2008) Comprehensive analysis of Affymetrix exon arrays using BioConductor. PLoS Computational Biology 4: e6.
9. Yates T, Okoniewski MJ, Miller CJ (2007) X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic Acids Research. 1-7.
10. Harris A (2002) Hypoxia - a key regulatory factor in tumour growth. Nature Reviews Cancer 2: 38-47.
11. Harper SJ, Bates DO (2008) VEGF-A splicing: the key to anti-angiogenic therapeutics? Nature Reviews Cancer 8: 880-887.
12. Barathova M, Takacova M, Holotnakova T, Gibadulinova A, Ohradanova A, et al. (2008) Alternative splicing variant of the hypoxia marker carbonic anhydrase IX expressed independently of hypoxia and tumour phenotype. Br J Cancer 98: 129-136.
13. Srinivasan K (2005) Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods 37: 345-359.
14. Shah S, Pallas JA (2009) Identifying differential exon splicing using linear models and correlation coefficients. BMC Bioinformatics 10: 26-32.
15. Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, et al. (2008) FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics 24: 1707-17014.
16. Xing Y, Stoilov R, Kapur K (2008) Mads: A new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA 14: 1470-1479.
17. French PJ, Peeters J, Horsman S, Duijm E, Siccama I, et al. (2007) Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. Cancer Research 67: 5635-5642.
18. Schutte M, Elstrodt F, Bralten LBC, Nagel JHA, Duijm E, et al. (2008) Exon expression arrays as a tool to identify new cancer genes. PLoS one 3: e3007.
19. Winter SC, Buffa FM, Silva P, Miller C, Valentine HR, et al. (2007) Relation of a hypoxia metagene derived from head and neck cancer to prognosis of multiple cancers. Cancer Res 67: 3441-3449.
20. Clark TA, Schweitzer AC, Chen TX, Staples MK, Lu G, et al. (2007) Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biology 8: R64.
21. Affymetrix. Exon array background correction,Affymetrix Whitepaper, available: http://www.affymetrix.com/support/technical/whitepapers/ exon-background-correction-whitepaper.pdf.
22. Greijer AE, van der Greop P, Kemming D, Shvarts S, Semenza GL, et al. (2005) Up-regulation of gene expression by hypoxia is mediated predominantly by hypoxia-inducible factor 1 (HIF-1). Journal of Pathology 3: 291-304.
23. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protocols 4: 44-57.
24. Deniss GJ, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biology 4: P3.
25. Marinkovich MP (2008) Laminin 332 in squamous-cell carcinoma. Nat Rev Cancer 7: 370-380.
26. Ono Y, Nakanishi Y, Ino Y, Niki T, Yamada T, et al. (1999) Clinicopathologic significance of laminin-5 γ2 chain expression in squamous cell carcinoma of the tongue. Cancer 85: 2315-21.
27. Skyldberg B, Salo S, Eriksson E, Aspenblad U, Moberger B, et al. (1999) Laminin-5 as a marker of invasiveness in cervical lesions. J Natl Cancer Inst 91: 1882-7.
28. Yamamoto H, Itoh F, Iku S, Hosokawa M, Imai K (2001) Expression of the γ 2 chain of laminin-5 at the invasive front is associated with recurrence and poor prognosis in human esophageal squamous cell carcinoma. Clin Cancer Res 7: 896-900.
29. Ferrigno O, Virolle T, Galliano MF, Chauvin N, Ortonne JP, et al. (1997) Murine laminin α 3a and α 3b isofrom chains are generated by usage of two promoters and alternative splicing. J of Biological Chemistry 272: 20502-20507.
30. Moller-Levet CS, West C, Miller CJ (2007) Exploiting sample variability to enhance multivariate analysis of microarray data. Bioinformatics 23: 2733-2740.
31. Jolliffe IT (1986) Principal Component Analysis. New York, USA: Springer.
32. Liu WM, Mei R, Di X, Ryder T, Hubbell E, et al. (2002) Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 18: 1593-1599.
33. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Research 30: 207-210.
34. Irizarry RA (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
35. Beffa CD, Cordero F, Calogero RA (2008) Dissecting an alternative splicing analysis workflow for GeneChip (R) Exon 1.0 ST Affymetrix arrays. BMC Genomics 9: 571.
36. Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. J R Statis Soc 57: 289-300.
37. Modrek B, CL (2002) A genomic view of alternative splicing. Nature Genetics 30: 13-19.
38. Affymetrix. Identifying and validating alternative splicing events,Technical Note, available: http://www.affymetrix.com/support/technical/ technotes/id-altsplicingevents-technote.pdf.
39. Vandesompele J, de Preter K, Pattyn F, Poppe B, van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 3: 0034.1-0034.11.
40. -ΔΔCT method. Methods 25: 402-408.
41. Robinson MD, Speed TP (2007) A comparison of Affymetrix gene expression arrays. BMC Bioinformatics 8: 449.
42. Fitsialos G, Bourget I, Augier S, Ginouves A, Rezzonico R, et al. (2008) HIF1 transcription factor regulates laminin-332 expression and keratinocyte migration. Journal of cell science 121: 2992-3001.
43. O'Toole EA, Marinkovitch MP, Peavey CL, Ameiva M, Furthmayr H, et al. (1997) Hypoxia increases human keratinocyte motility on connective tissue. Journal of Clinical Investigation 100: 2881-2891.
44. Ortiz-Urda S, Garcia J, Green CL, Chen L, Lin Q, et al. (2005) Type VII collagen is required for Ras-driven huma epidermal tumorigenesis. Science 307: 1773-1776.