Biological determinants of bladder cancer gene expression subtypes

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Aine, Mattias ^a   Eriksson, Pontus ^a   Liedberg, Fredrik ^b   Sjödahl, Gottfrid ^b   Höglund, Mattias ^a  

^a LUND UNIVERSITY   (Sweden)

^b LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

BLADDER TUMOR; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; PATHOLOGY;

BIOMARKERS, TUMOR; DATABASES, GENETIC; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; URINARY BLADDER NEOPLASMS;

EID: 84930959056     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep10957     Document Type: Article

References (53)

1. Epstein, J. I., Amin, M. B., Reuter, V. R. & Mostofi, F. K. The World Health Organization/International Society of Urological Pathology consensus classification of urothelial (transitional cell) neoplasms of the urinary bladder. Bladder Consensus Conference Committee. Am J Surg Pathol 22, 1435-48 (1998).
2. Fujimoto, K. et al. Frequent association of p53 gene mutation in invasive bladder cancer. Cancer Res 52, 1393-8 (1992).
3. van Rhijn, B. W. et al. The fibroblast growth factor receptor 3 (FGFR3) mutation is a strong indicator of superficial bladder cancer with low recurrence rate. Cancer Res 61, 1265-8 (2001).
4. Dalbagni, G., Presti, J., Reuter, V., Fair, W. R. & Cordon-Cardo, C. Genetic alterations in bladder cancer. Lancet 342, 469-71 (1993).
5. Knowles, M. A. et al. Allelotype of human bladder cancer. Cancer Res 54, 531-8 (1994).
6. Orlow, I. et al. Deletion of the p16 and p15 genes in human bladder tumors. J Natl Cancer Inst 87, 1524-9 (1995).
7. Presti, J. C., Jr., Reuter, V. E., Galan, T., Fair, W. R. & Cordon-Cardo, C. Molecular genetic alterations in superficial and locally advanced human bladder cancer. Cancer Res 51, 5405-9 (1991).
8. Richter, J. et al. Marked genetic differences between stage pTa and stage pT1 papillary bladder cancer detected by comparative genomic hybridization. Cancer Res 57, 2860-4 (1997).
9. Bakkar, A. A. et al. FGFR3 and TP53 gene mutations define two distinct pathways in urothelial cell carcinoma of the bladder. Cancer Res 63, 8108-12 (2003).
10. van Rhijn, B. W. et al. FGFR3 and P53 characterize alternative genetic pathways in the pathogenesis of urothelial cell carcinoma. Cancer Res 64, 1911-4 (2004).
11. Wu, X. R. Urothelial tumorigenesis: a tale of divergent pathways. Nat Rev Cancer 5, 713-25 (2005).
12. Blaveri, E. et al. Bladder cancer outcome and subtype classification by gene expression. Clin Cancer Res 11, 4044-55 (2005).
13. Dyrskjot, L. et al. Identifying distinct classes of bladder carcinoma using microarrays. Nat Genet 33, 90-6 (2003).
14. Sanchez-Carbayo, M., Socci, N. D., Lozano, J., Saint, F. & Cordon-Cardo, C. Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays. J Clin Oncol 24, 778-89 (2006).
15. Lauss, M., Ringner, M. & Hoglund, M. Prediction of stage, grade, and survival in bladder cancer using genome-wide expression data: a validation study. Clin Cancer Res 16, 4421-33 (2010).
16. Lindgren, D. et al. Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome. Cancer Res 70, 3463-72 (2010).
17. Lindgren, D. et al. Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma. PLoS One 7, e38863 (2012).
18. Harbst, K. et al. Molecular profiling reveals low-and high-grade forms of primary melanoma. Clin Cancer Res 18, 4026-36 (2012).
19. Perou, C. M. et al. Molecular portraits of human breast tumours. Nature 406, 747-52 (2000).
20. Sadanandam, A. et al. A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med 19, 619-25 (2013).
21. Sorlie, T. et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 98, 10869-74 (2001).
22. Choi, W. et al. Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. Cancer Cell 25, 152-65 (2014).
23. Damrauer, J. S. et al. Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology. Proc Natl Acad Sci U S A 111, 3110-5 (2014).
24. Sjodahl, G. et al. A molecular taxonomy for urothelial carcinoma. Clin Cancer Res 18, 3377-86 (2012).
25. Sjodahl, G. et al. Toward a molecular pathologic classification of urothelial carcinoma. Am J Pathol 183, 681-91 (2013).
26. The Cancer Genome Atlas Project Consortium. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507, 315-22 (2014).
27. Monti, S., Tamayo, P., Mesirov, J. & Golub, T. Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data. Machine Learning 52, 91-118 (2003).
28. Wilkerson, M. D. & Hayes, D. N. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics 26, 1572-3 (2010).
29. Carbon, S. et al. AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288-9 (2009).
30. Lianes, P. et al. Altered patterns of MDM2 and TP53 expression in human bladder cancer. J Natl Cancer Inst 86, 1325-30 (1994).
31. Kuzmichev, A. N. et al. Sox2 acts through Sox21 to regulate transcription in pluripotent and differentiated cells. Curr Biol 22, 1705-10 (2012).
32. Sandberg, M., Kallstrom, M. & Muhr, J. Sox21 promotes the progression of vertebrate neurogenesis. Nat Neurosci 8, 995-1001 (2005).
33. Abrahams, N. A., Moran, C., Reyes, A. O., Siefker-Radtke, A. & Ayala, A. G. Small cell carcinoma of the bladder: a contemporary clinicopathological study of 51 cases. Histopathology 46, 57-63 (2005).
34. Alijo Serrano, F., Sanchez-Mora, N., Angel Arranz, J., Hernandez, C. & Alvarez-Fernandez, E. Large cell and small cell neuroendocrine bladder carcinoma: immunohistochemical and outcome study in a single institution. Am J Clin Pathol 128, 733-9 (2007).
35. Jones, T. D. et al. Thyroid transcription factor 1 expression in small cell carcinoma of the urinary bladder: an immunohistochemical profile of 44 cases. Hum Pathol 36, 718-23 (2005).
36. Taupenot, L., Harper, K. L. & O'Connor, D. T. The chromogranin-secretogranin family. N Engl J Med 348, 1134-49 (2003).
37. Gandhi, D. et al. Retinoid signaling in progenitors controls specification and regeneration of the urothelium. Dev Cell 26, 469-82 (2013).
38. Shin, K. et al. Hedgehog/Wnt feedback supports regenerative proliferation of epithelial stem cells in bladder. Nature 472, 110-4 (2011).
39. Shin, K. et al. Cellular origin of bladder neoplasia and tissue dynamics of its progression to invasive carcinoma. Nat Cell Biol 16, 469-78 (2014).
40. Shin, K. et al. Hedgehog signaling restrains bladder cancer progression by eliciting stromal production of urothelial differentiation factors. Cancer Cell 26, 521-33 (2014).
41. Van Batavia, J. et al. Bladder cancers arise from distinct urothelial sub-populations. Nat Cell Biol 16, 982-91, 1-5 (2014).
42. Vortkamp, A. et al. Regulation of rate of cartilage differentiation by Indian hedgehog and PTH-related protein. Science 273, 613-22 (1996).
43. Ruiz-Perez, V. L. et al. Evc is a positive mediator of Ihh-regulated bone growth that localises at the base of chondrocyte cilia. Development 134, 2903-12 (2007).
44. Dale, J. K. et al. Cooperation of BMP7 and SHH in the induction of forebrain ventral midline cells by prechordal mesoderm. Cell 90, 257-69 (1997).
45. Liem, K. F., Jr., Tremml, G., Roelink, H. & Jessell, T. M. Dorsal differentiation of neural plate cells induced by BMP-mediated signals from epidermal ectoderm. Cell 82, 969-79 (1995).
46. Yang, Y. et al. Relationship between dose, distance and time in Sonic Hedgehog-mediated regulation of anteroposterior polarity in the chick limb. Development 124, 4393-404 (1997).
47. Scherz, P. J., Harfe, B. D., McMahon, A. P. & Tabin, C. J. The limb bud Shh-Fgf feedback loop is terminated by expansion of former ZPA cells. Science 305, 396-9 (2004).
48. Verheyden, J. M. & Sun, X. An Fgf/Gremlin inhibitory feedback loop triggers termination of limb bud outgrowth. Nature 454, 638-41 (2008).
49. DeGraff, D. J. et al. When urothelial differentiation pathways go wrong: implications for bladder cancer development and progression. Urol Oncol 31, 802-11 (2013).
50. Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).
51. Gray, K. A., Yates, B., Seal, R. L., Wright, M. W. & Bruford, E. A. Genenames.org: the HGNC resources in 2015. Nucleic Acids Res. doi:10.1093/nar/gku1071 (2014).
52. R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2014).
53. Benjamini, Y. & Hochberg, Y. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57, 289-300 (1995).