A novel transcript, VNN1-AB, as a biomarker for colorectal cancer

International Journal of Cancer

Volumn 135, Issue 9, 2014, Pages 2077-2084

  Løvf, Marthe ^a,b,c   Nome, Torfinn ^a,b   Bruun, Jarle ^a,b   Eknæs, Mette ^a,b   Bakken, Anne C ^a,b   Mpindi, John P ^d   Kilpinen, Sami ^d,e   Rognum, Torleiv O ^c,f   Nesbakken, Arild ^b,g   Kallioniemi, Olli ^d   Lothe, Ragnhild A ^a,b,c   Skotheim, Rolf I ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c UNIVERSITY OF OSLO   (Norway)

^d UNIVERSITY OF HELSINKI   (Finland)

^e MediSapiens Ltd   (Finland)

^f NORWEGIAN INSTITUTE OF PUBLIC HEALTH   (Norway)

^g AKER UNIVERSITY HOSPITAL   (Norway)

Author keywords

alternative splicing; biomarker; colorectal cancer; transcriptome; VNN1

Indexed keywords

TRANSCRIPTOME; TUMOR MARKER;

ARTICLE; COLORECTAL CANCER; CONTROLLED STUDY; EXON; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; HUMAN TISSUE; MAJOR CLINICAL STUDY; MICROSATELLITE INSTABILITY; MOLECULAR CLONING; MORPHOLOGY; ONCOGENE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ALIGNMENT; TRANSCRIPTOMICS; VNN1 AB GENE;

ALTERNATIVE SPLICING; BIOMARKER; COLORECTAL CANCER; TRANSCRIPTOME; VNN1;

ADENOMA; ALTERNATIVE SPLICING; AMIDOHYDROLASES; COLON; COLORECTAL NEOPLASMS; EXONS; GENE EXPRESSION PROFILING; GPI-LINKED PROTEINS; HUMANS; NEOPLASM STAGING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; TUMOR CELLS, CULTURED; TUMOR MARKERS, BIOLOGICAL;

EID: 84906240779     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.28855     Document Type: Article

References (28)

1. Ferlay J, Shin HR, Bray F, et al. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 2010; 127: 2893-917.
2. O'Connell JB, Maggard MA, Ko CY,. Colon cancer survival rates with the new American Joint Committee on Cancer sixth edition staging. J Natl Cancer Inst 2004; 96: 1420-5.
3. Fearon ER, Vogelstein B,. A genetic model for colorectal tumorigenesis. Cell 1990; 61: 759-67.
4. Guastadisegni C, Colafranceschi M, Ottini L, et al. Microsatellite instability as a marker of prognosis and response to therapy: a meta-analysis of colorectal cancer survival data. Eur J Cancer 2010; 46: 2788-98.
5. Skotheim RI, Nees M,. Alternative splicing in cancer: noise, functional, or systematic? Int J Biochem Cell Biol 2007; 39: 1432-49.
6. Davuluri RV, Suzuki Y, Sugano S, et al. The functional consequences of alternative promoter use in mammalian genomes. Trends Genet 2008; 24: 167-77.
7. Agarwal VR, Bulun SE, Leitch M, et al. Use of alternative promoters to express the aromatase cytochrome P450 (CYP19) gene in breast adipose tissues of cancer-free and breast cancer patients. J Clin Endocrinol Metab 1996; 81: 3843-9.
8. Nakanishi T, Bailey-Dell KJ, Hassel BA, et al. Novel 5' untranslated region variants of BCRP mRNA are differentially expressed in drug-selected cancer cells and in normal human tissues: implications for drug resistance, tissue-specific expression, and alternative promoter usage. Cancer Res 2006; 66: 5007-11.
9. Slamon DJ, Clark GM, Wong SG, et al. Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 1987; 235: 177-82.
10. Gianni L, Dafni U, Gelber RD, et al. Treatment with trastuzumab for 1 year after adjuvant chemotherapy in patients with HER2-positive early breast cancer: a 4-year follow-up of a randomised controlled trial. Lancet Oncol 2011; 12: 236-44.
11. Tomlins SA, Rhodes DR, Perner S, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005; 310: 644-8.
12. Mpindi JP, Sara H, Haapa-Paananen S, et al. GTI: a novel algorithm for identifying outlier gene expression profiles from integrated microarray datasets. PLoS One 2011; 6: e17259.
13. Tibshirani R, Hastie T,. Outlier sums for differential gene expression analysis. Biostatistics 2007; 8: 2-8.
14. Wu B,. Cancer outlier differential gene expression detection. Biostatistics 2007; 8: 566-75.
15. Berg M, Danielsen SA, Ahlquist T, et al. DNA sequence profiles of the colorectal cancer critical gene set KRAS-BRAF-PIK3CA-PTEN-TP53 related to age at disease onset. PLoS One 2010; 5: e13978.
16. Thorstensen L, Diep CB, Meling GI, et al. WNT1 inducible signaling pathway protein 3, WISP-3, a novel target gene in colorectal carcinomas with microsatellite instability. Gastroenterology 2001; 121: 1275-80.
17. Kilpinen S, Autio R, Ojala K, et al. Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol 2008; 19: R139.
18. Nome T, Thomassen GO, Bruun J, et al. Common fusion transcripts identified in colorectal cancer cell lines by high-throughput RNA sequencing. Transl Oncol 2013; 6: 546-53.
19. Trapnell C, Pachter L, Salzberg SL,. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25: 1105-11.
20. Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25.
21. Rozen S, Skaletsky H,. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000; 132: 365-86.
22. Lind GE, Danielsen SA, Ahlquist T, et al. Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Mol Cancer 2011; 10: 85.
23. Ransohoff DF,. Cancer: developing molecular biomarkers for cancer. Science 2003; 299: 1679-80.
24. Sveen A, Bakken AC, Agesen TH, et al. The exon-level biomarker SLC39A14 has organ-confined cancer-specificity in colorectal cancer. Int J Cancer 2012; 131: 1479-85.
25. Marshall KW, Mohr S, Khettabi FE, et al. A blood-based biomarker panel for stratifying current risk for colorectal cancer. Int J Cancer 2010; 126: 1177-86.
26. Yip KT, Das PK, Suria D, et al. A case-controlled validation study of a blood-based seven-gene biomarker panel for colorectal cancer in Malaysia. J Exp Clin Cancer Res 2010; 29: 128.
27. Gensollen T, Bourges C, Rihet P, et al. Functional polymorphisms in the regulatory regions of the VNN1 gene are associated with susceptibility to inflammatory bowel diseases. Inflamm Bowel Dis 2013; 19: 2315-25.
28. Huang H, Dong X, Kang MX, et al. Novel blood biomarkers of pancreatic cancer-associated diabetes mellitus identified by peripheral blood-based gene expression profiles. Am J Gastroenterol 2010; 105: 1661-9.